Yes, you absolutely need a fire control to fire missiles at waypoints.  Fortunately, a .1 HS fire control is sufficient.

I have to say, using missiles to scout systems is a bit of a mixed bag.

I am experimenting with both single stage missiles and 2-stage ones.  The advantage of the 2-stage ones is that the sensor will stay on location indefinitely, but you pay the research cost twice.

So far, EM missiles seem to work better than active sensor missiles in detecting enemies at range.  I am waiting on the next level of Thermal Sensors to build thermal sensor probes.

The problem is that scouting a whole system is rather expensive.  Both in terms of missiles, and in the fact that my probe ship has to keep flying back to base to get more missiles.  So I think I will reserve missile scouting for systems in which I actually detected a hostile ship, in order to localize them, find out how many and what type of ship they have, and information on the range of their AMMs.

My MSP 3 active sensor missile was detected and destroyed at 2.3 times the range of the sensor.  That suggests that an MSP 6 missile, (at least once I get better sensors or even power plants) would be able to detect the enemy ships that shoot it down.  So if I am trying for real information, as distinct from detecting the mere presence of the enemy, designing a missile that can identity number and class of the enemy before being destroyed might be worth it.  Above 6 MSP, the enemy's detection range of my probes is going to increase faster than the range of the sensors on my probes increases.

I wonder if it is worth making a 2-stage missile, where the separation range is greater than the enemy's apparent AMM range, possibly with a very efficient 100 km/s engine on the 2nd stage.

I am trying to figure out what useful information I can get from missiles, and how to make use of it.  I am pretty sure I could use them to detect when the enemy moves out, which would give an idea as to what range their planetary or other passive sensors had.

I swear I have done it in the past. I'll load up my test game and have a poke around.
Edit:
Well this is weird. I Can load and fire missiles from the PDC's fine. However the geo survey points just refuse to go down.
Process was this:
 Create new conventional game, spacemaster transnewtonian research, and geo survey sensors, space master a size 1 conventional engine.
Design a missile with 10 MSP of geo survey sensor, 6.8 fuel capacty, and 7 engines (also contains .2 reactor for the sensors). Create the missile then spacemaster the design.
Open the missile base design, change ordnance to the new missiles.
Open up one of the missile bases, click "standard" reload.
Open the system map and create a waypoint at the moon. use the SB waypoint button which puts a waypoint on the body which moves with the body.
Then select and fire at the waypoint, watch the missile slowly crawl at 100km/s towards the moon, eventually it gets there, but the body stays at 173 survey points.

Well, I did get the missiles to load in the PDC, that part works.  But the sticking point is still firing them.

And the next sticking point is figuring out a good way to make recon drones in general more easy to use.  Also, I will want to see if when you use more than one, the points stack.  Because then you could just build LOTS of small buoys, and just use multiples on planets and big moons to get the survey done in a reasonable amount of time.

(edit)  12 days later, still suffering the effects of 'transit'.  Now the 'missile launch' button SAYS that it is what you use when you are launching without using a fire control, but I seem to be missing something to get it to work.

IIRC there should be hard wired 5 or 15 min interval for PDC firing at he same body, so that other races there have time to respond to "nuclear war". This simulates the time the ICBM needs to fly through upper atmosphere to any other colony on the same body. Otherwise it would be instant (5s), with target distance of 0 km. Maybe that's also why it is showing you that "transit effect".

It could be a size issue, in that the ICBM Silo in the conventional missile bases do not accept anything else but Size 24. I'm currently playing a 3-way conventional Earth start campaign and one of the powers created TN missiles to use in them. I had no trouble loading them:



I haven't tried with smaller sizes. With normal launchers, that isn't a problem but the ICBM Silo might be a special case.

if all else fails you can abandon ship in the ships screen

If all else fails you can call government of your country and ask them to help you load ICBM to your ICBM launcher

When I say scrap I mean delete them after making replacements :/

I saw the refit PDC, but no scrap option.   Oh well, an update.  So I got Aurora back working, made geosurvey missiles, and still can't load them.  I see them on the load from population window, but can't assign them to the launch, it says "select a missile type".

Well, I built it using the missile design tech, so it should be a missile.  Somewhere there is a button that does what I want it to...