Only at the very first levels. ( First level is Efficiency 3 for both meaning you have 33% left for all other systems if you equip both )
At for example 5:th tech level you will have Efficiency 8 on both meaning you can make a ship with 75% left for all other systems if both are equipped. Basically you could even equip all your warships with it ( even if it would be costly it is within reach ).
At max tech levels ( Efficiency 15 ) You would need to allocate just 13% of your ship to both these systems leaving the remaining 87% free.
For balance any "Raiding" or "Scouting" Jump drive or what you want to call it would need to have a much flatter progression curve in tech, or be made so much significantly more expensive in resources that it's not feasible to equip large parts of your fleet with it.
I still think the Jump drive needs a buff (Move it up a tech level or two) to make room for the second drive early enough if you want it available somewhere in the midgame where cloaks become available. The cloak progression line could also be flattened out, with a size reduction for less efficient cloaks. So you can build small, reduced efficiency cloaks.
That's a good idea, and one that I have suggested before. The tricky question is how you don't make it unbalanced ( Basically what prevents everyone from always using just passive targeting? ). It needs to have some serious downsides too besides requiring a 0.25 msp sensor in each missile.
For one active sensors should outrange thermal sensors, and if you fire at an EM target, your enemy always may turn off their emissions. A further downside could be that your homing missiles pick their targets themselves, any they can detect, which may not be the one you intended. So in a fleet battle this will lead to very poor focus firing.
If you want, you could also give missiles a to-hit modifier depending on the sensor strength and range, but for consistency MFC should be affected by this too. So active sensor head missiles would be more accurate than passive sensor head missiles, and active ship targeting should be more accurate than sensor head missiles, and combined active ship targeting+ sensor head would be most accurate. Please note if you throw in ECCM and ECM on a missile, you are already using up 0.75 MSP, which will definitely push up missile size. ECCM seems like a must, you cannot accept a -20 or -30 % hit chance decrease.
If you wanted to give a serious downside to self targeting missiles, gives CIWS a significant bonus to hit against sensor equipped missiles. Something about how they're lighting themselves up with the sensor package pinging off. Then you could justify buffing the effective range of missile sensors. So for your big warships, if you want to get your warheads through a heavy missile defense in a proper fleet, you guide them in from a directed fire control. But if your picking off a lone merchant ship, or a handful of troop ships in a surprise attack, the trade off of using more missiles to achieve the same effective damage may be worth it.
Passive sensors don't light up, by definition of passive sensors. I also really dislike the idea of giving CIWS a bonus compared to other missile defenses. I for one only install CIWS on civilians, supply ships, my warships have dedicated firecontrol+sensor+guns arrangements for defense.