I always use commercial drives on my survey ships. They're intended to be deployed for extreme duration anyway, and so commercial makes fuel consumption extremely small. Yes, they're slow, but they can run for *years*.
Because any ship with a survey sensor is a military ship, you must pay for ship maintenance.
The average annual MSP cost for overhauling a ship that is always either deployed or in overhaul is 20% of the ship's BP (four years at 0 MSP/YR plus 1 year at MSP/YR = BP).
Therefore using large commercial drives ends up costing more in the long run than cheaper, smaller military drives that achieve the same ship speed.
Of course, a large commercial drive uses a LOT less fuel than the smaller military drive that achieves the same ship speed.
But I find that my survey fleet is rather a small fraction of my total fuel usage (at least, after I've colonized a few systems).
I usually use an engine with 55% efficiency so i can use a smaller military JD to try and compact my design as much as possible
You could just make your engine smaller. Anything under 25HS is a military engine.
Use multiples if you like, but this way you can keep your power rating down to conserve fuel, and still enjoy the benefit of the compact military JD.
In fact, I go really small for surveyors.
At Improved Nuclear Thermal tech, I make 500t surveyors.
Each has a 110t engine @65% power.
They travel 916km/s.
Slow, sure, but they spend more time surveying than moving. (I play with Survey Speed at 10%.)
For transiting between systems, I research a 1kt mil JD and slap it on a tiny station (298t, with a 5-ton active sensor and 12.5t of eng spaces included).
I drag the stations into place with a 1kt tug that uses two of the same 110t@65% engines. (I could research a separate (more optimal) engine for this ship if I really wanted to).
It travels 915km/s (705 while tugging the jump station).
Slow, but who cares? The surveyors don't need the gate in place until they are done in the current system anyway.
It can tug a jump station 13.36Bkm and still have enough fuel for the return trip.
Since I can build the jump station with fighter factories (3 ffacts can make one jump station in just over 6 months), my tugs usually don't have to travel very far between trips. (I tend to have forward operating colonies one system behind the survey fleet.)
And since a mil JD is a commercial component, those jump stations don't need any maintenance.
Drop 'em off and forget about 'em.
The tug needs maintenance, but it has plenty of time for overhauling between runs.