Active sensors are down for a certain period of time I thought, but your passives work fine. Your fire controls are what are really messed up. I'm not sure about CIWS.
The big difference though is if you use "standard transit" or "squadron transit"
Standard Transit disables sensors and fire controls for a fixed 5 min interval. Your ships arrive exactly on the jump point. All ships in the formation can transit at once so long as at least one jump engine equiped ship is on the jump point (either side). The jump engine has to be able to transit the ships that make up the formation though. So you can't send through a 30,000 tonne ship with a 3000 tonne jump engine tender (or at least I don't think that is possible).
Squadron Transit disables sensors and fire controls for a variable amount of time, and I don't know what determines it, but seems to be around 30 seconds or so. Your ships arrive scattered around the jump point at variable distances up to the maximum distance your jump drive allows. I don't know any details of how the distance is selected as I've never looked in detail at arrival positions. I assume angular arrival is purely random but the distance might be anything (bell curved or whatever). Jump engine limitations are enforced per formation, so a starting jump engine can bring over 2 other ships. This requires you break up your formations usually.