Who doesn't have CIWS?

If you play a conventional start, you will not have CIWS unless you invest a sizeable amount of time in their research. And since they are very sub-par when it comes to battle fleets (area PD weapons or AMM missiles are king for fleets PD, compared to CIWS who are more effective for ships who operate alone), they usually take the backburner. Thus, it is quite possible to either not have them, or to have them at a low tech level. In that case, railgun or laser turrets are better, or your only choice.

Well, I sort of assume that they get there on abstracted civilian craft that the game doesn't model... yet. 

You are obviously free to play how you want, and I don't want to force my view on others.
It's just that in a game where I can't even have minerals on another planet unless I manually carry them with MY ships (civs won't move minerals), I cannot simply justify the fact that some "abstracted civilian crafts" are carrying my geological teams to prospect planets in a system 3 jumps away, where there's simply nothing a civilian ship would ever want.
So no, no teleporting for my teams

Examples?

There's too many to count. Example #1 would be overreliance on missiles, which some players even use as their ONLY weapon. No sane political power would ever do this, even more so in the case of box launchers, because they are easily counterable.
Yes it works on the AI of course, and missiles are a very valid weapon. Worthy of being a sizeable part of your fleet. But as your only weapon?  Real enemies would adapt quickly, either sending massive PD fleets OR "soaker" armored fleets to eat through your missiles and get close to kill you.
The same reasoning can be done for some fighter designs which I have seen posted in the forums. Or really, for any over-reliance on super-specialized designs, which once again work on the AI because it can't adapt.

When creating a ship, I always ask myself 4 questions:
Would the USA build and use such a ship? If the answer is no, back to the drawing board.
Would China build and use such a ship? If the answer is no, back to the drawing board.
Would Russia build and use such a ship? If the answer is no, back to the drawing board.
Would a 10 year old child be able to easily build a cheap counter to this ship? If the answer is yes, back to the drawing board.

You should definitely think of what you NEED to do with your tankers and then build them with specs that satisfy your needs. This is especially true for speed and for amount of fuel they carry. If you expect them to go into possibly dangerous territory, some armor and CIWS (or railguns/lasers if you don't have CIWS) are also good.

Regarding deployment times, personally, I try not to abuse the system, at the cost of efficiency. I try to make it so things are realistic, and so I put an appropriate length for deployment. I find it more... satisfying, to know I did not game the system.

But that is just me, I won't judge people who minmax. Setting 3 months is allowed by the system, so... If you want to do it just do it. It's just that to me RP is THE golden rule by which I play this game. It is the thing that gives me the most fun.

For example since teleport does not exist in this setting, I have ships ferrying around geological teams AND spy teams (dangerous proposition this one, often ends bad but I try it when I can, and when I can't I just don't spy on enemies).

For example I don't make fighters with years of maintenance time (because a human confined in a cockpit for years would go mad).

For example I don't build some type of minmaxed military ships that no sane real nation would ever make. Because while they might work against the AI which is stupid and can't counter them, no sane real nation would build them knowing they are so easily countered...

My own view for commercial ships is that this is a classic example of rp vs power gaming. Sure, I can set this to 3 months for gas giant fuel harvesting, but is that actually realistic or fair? So i always set it to what I think the maximum mission time will be (ie 5 years for fuel harvesting). And if I miss my target then I'll do my best to bring that poor crew home asap. Anything else feels like exploiting the game.

That being said I have occasionally broken the rule with a hand-waving "crew rotation" justification, but only for very special circumstances.

I doubt i'll have to worry about defences for now, I only recently generated an NPR via SpaceMaster mode, and even then I still haven't found it, I just want a fuel tanker so that the ships that go on other systems don't run out of fuel on me

Figure out the mission first.  How do you keep your tankers safe?  With speed?  Small size and hard to detect?  Enough sensors so as to be comfortably behind the battle line?

What do they have to keep up with and refuel?  Fighters? LACs?  Hefty battle fleets?

For fighters, you want a fighter-tanker of the same speed and size as your other fighters, and it can fly with the attack squadron, refuel them midway, fly back to the carrier/tanker, then meet the returning fighters midway again.

If you are using small size as a defense, then your tankers need to fly in a squadron with a sensor ship and armed escort of the same size and speed.

If you are are building a carrier with a huge fuel supply, you are inescapably a big target, hopefully not an exposed one.

A thing to consider:  If you are already choosing the large size option with a lot of engines, add a tractor beam to it.  As a jump tender, it is already either the largest or tied for largest ship in the expedition anyway.

Thanks, you all, however I have an important question, how much is the Deployement Time supposed to be?

For fuel tankers?

• If there are roleplaying considerations, whatever those require. ("All ships of the xkg't*!lh Mageocracy must have a Deployment Time of exactly 11.42 months." "I try to give everything enough Deployment Time to handle their expected missions, even when the game mechanics don't enforce it.")
• If your primary design goal for the class is 'tiny' (usually meaning a support boat to let your fighter wing go further) then either the smallest value the program will register, or as much as you can squeeze in without going over your weight limit (if it needs to react under combat conditions).
• For every other case (so probably 99% or more of the time) you want three months, so it can qualify as commercial.

Hard to say without knowing details.

For example, 10 months deployment and a year of maintenance life suits me for many ships that are supposed to be capable of extended operations. Maintenance is a little longer because having something blow up is more embarrassing than having a cranky crew, and because I'd like to have a reserve for repairs if I get into a fight at the end of an extended mission.

But if you have many frontier populations while only your homeworld has maintenance facilities, your frontier patrol may want ships that have years of maintenance life but only a month of deployment time or so.

And sometimes it's not a question what you need, but what you can get cheaply. An AMM base using box launchers requires very little crew and engineering spaces to have a mission life of years to decades. The option to dump them anywhere and forget about them is nice to have even if you don't intend to do so.