The amount of required battleships is too damn high. That's why a lot of sieges take place when someone discovers that a base is poorly supplied. Cloaked supply transports would be yet another lazy "panicbutton", alongside the rules regarding base attack declaration and whatnot.
----Off-topic rant----
It's the idea that base supply somehow equates to work and thus have value that needs protecting that's the core of the problem. In my view, value should be judged on roleplay and dynamic interactions, not the amount of time that went into creating it. Afterall, it takes countless hours of practice to create a PVP-whore, should they get special treatment and special rules to protect their "investment"?
Bases were the final nail, worse than Gallia, because it changed the game away from being a space shooter to be space farmville and player mentality went right down the drain with it. Let all the POB's burn.