While the cargo limit of the equipment themselves prevents you from simply mounting everything on a battleship and doing whatever you wish, everything apart from Docking Modules use fuel to power themselves.
For cloaks, a CAU8 LAC still has something like 1500 cargo space free which, using MOX, is 25 minutes of cloaking which I'd guess was viewed as far too long - shorter bursts are the tactics encouraged. They also added the ability to stop the cloaking sequence with a CD so having many opportunities to cloak and move around undetected. Cloaks remove your CM capabilities as well, so you're a lot more susceptible to missiles and CDing.
However, the fuel will be changed to an ammo-based commodity from what I heard of the devs' plans. The cargo space remains to prevent them being used on small ships, while the actual cargo limit for smaller cloaks prevents them being used on larger ships.
Jumpdrive Mk IVs are not intended to allow solo jumping, the high cargo space require at least one transport to fuel the fleet's jump. Mk II and III are not really that different in cargo consumption (other than over time). However, the Mk III is intended for Battleships only, using the powercore requirement - likely it is a 'lore' decision for the power required to be above that of cruisers. Battlecruisers can just use Mk IIs and no more.
Hyperspace Scanners aren't really needed to actually have equipped all the time, since you can just type in the coordinates gathered in the past. Battlecruisers are actually pretty good at this with enough space to do a scan. Most Cruisers can at least mount one scanner module, The power limit here is to stop transports flying around gathering several sets of coordinates in one cargo hold's worth. Gunboats don't have the slot since they are not intended to scan either.
I would agree with you about reducing the cargo requirement for Docking Modules though, making heavy use of them on Carriers available without making their use of cloaks too great (by increasing the ship's cargo hold for example).
