I would personally get rid of ELINT Module and add one more of each survey sensor instead for faster survey. Ideally you want Science Department as well, it is 100 tons component so not that big. Other than that I think the design is fine.
I think you want your spying on separate ship, from my experience it takes quite some time to gather any data. In my current game I have alien homeworld under siege and one of my spy ships is watching over it and new data from ELINT are sparse (I have two ELINTs on the ship). Based on that I believe that chance you will gather something during survey of the system is low. And you don't want to stay in the system to spy on them with survey ship.
I haven't yet developed the science department component (my 10% research speed means a 10k project takes a loooong time to complete). That is on the list for future upgrades however.
I'm considering dropping the ELINT module. Originally I had 2x each of the geo and grav survey sensors instead of the ELINT. I haven't used ELINT much and just realized now that the ELINT range is only 17M km, which is very short for a ship this sized I think. So I will most likely replace the ELINT with larger EM and TH sensors, though the diplomacy module is another interesting option (but too large I think at size 1000? can't remember off the top of my head).
My primary motivation for equipping my geosurvey ship with large passive sensors is to keep it from blindly stumbling onto hostile NPRs, which happens regularly with my geosurvey ships UNLESS I first manually send a passive scout through each newly explored system. Manual scouting is a bit tedious once there are more than a handful of new systems available, hence my desire to combine that capability onto the geosurvey scout.
Traditionally I have used scout carriers with dedicated passive scouts, geo scouts, and grav scouts to explore new systems. This system works, but it becomes increasingly difficult to manage as the number of scout carriers grows and the number of potential new systems gets larger than about 100.
I see, well my approach is different and I guess it is influenced by the lack of micromanaging concern. In this meaning what is going to happen in 1.12 will help me a lot though.
I usually create an Admin called First Contact with the following structure:
ELINT ship x 4
Diplo Ship x 4
Explorers x 4
Another Admin called GEO Survey Operations within the First Contact Admin
Geosurvey Ships x 10 to 15 full auto survey mode
Another Admin called GRAV Survey Operations within the First Contact Admin
Gravsurvey Ships x 5 full auto survey mode
I proceed as per below:
Option A
Explorer Jumps in the system, deploys a sensor at JP (AS,EM and TH roughly 20/30mkm), I flag the new system as Alien Controlled regardless so no one flies in unauthorized
Explorer flies over most interesting planets and sit in the system for a few days/weeks
If system does not have any alien activity and marked as secure by flagging it out the Alien Occupied status and our survey ships will start flying in, if a new system is found rinse and repeat.
Option B
Explorer Jumps in the system, deploys a sensor at JP (AS,EM and TH roughly 20/30mkm), I flag the new system as Alien Controlled regardless so no one flies in unauthorized
Explorer flies over most interesting planets and sit in the system for a few days/weeks
If system does have any alien activity I maintain the Alien Occupied status and send out Diplomatic ships and ELINT if the aliens have shown no hostility towards our explorer
Couple of Tips
All these ships are better off with commercial engines as you don't want any military reading to mislead the NPR races. Exceptions could be made for Gravships and Geoships as you may want to keep these on a lower tonnage and out of aliens in general. Also all shall be designed with their own Jump Engines so that the automation will do the heavy lifting for you avoiding also to tug around tenders etc. You can then spare tenders for military operations where JGs are not available yet.