Actually StikkyPixie I think your idea is very very good!! I like the idea of establishing a baseline for the ammuntion, and your idea of a continuous line back to the homeworld is a unique and interesting one, in this way, the game plays pretty much as it does now, but introduces those instances where if the line is cut, then only a limited amount of ammunition remains to those fleets that are cut off. I like it alot and it sounds balanced and makes good sense. I dont believe it will increase the amount of time a game takes to play appreciably as those moments of ammunition cut off will require strategic planning on the players part, and small time addtions, but not unduly so, and it seems to me those times will make the play more "realistic" haha, if it is possible to have a far future space warfare scenario more "real". But i like it, it throws in a new element to consider, and as a teacher once said in an english class i took, any story is all about the limits and faults of the characters and how they overcome them. With the introduction of your supply lines idea into the game, it would make those times when i run out of ammuntion more intense and it becomes a "do something" point. If i didnt have that, i might merrily continue to go from planet to planet haphazardly and there is little or no "tension" until i reach the enemy in their corner of the system. But this way, the tension is more often, and can be established by something as small as local raiders, or pirates or indeed enemy forces that are attacking a planet you have left behind and not developed.
The game is long now, some games last for days at a time, that this doesnt seem to me to make it any more unbearable. As a matter of fact the reason the game is so long in the first place is because the players have said they want more realistic build times, more realistic research times, longer transit times between planets, or less money flow because it makes the options, ships and researches to realistic. Anyway, i like your idea alot. And would like to suggest an additional thought, which of course you may or may not agree with. But ever since HomeWorld i have liked the idea of limiting factors, like your supply lines, and like the "fuel" on the the fighters and the corvettes which of course required refueling. Or "foodstuffs", which of course wasnt in a game, but it sounds reasonable, which means we have to dock on an oxygen planet, say a terran planet every so often with "foodstuffs" and "oxygen" to replenish. In addition, there could be beam weapon "cores" (in effect crystals that have a certain life span, say 1800 seconds or 30 minutes? Or whatever seems reasonable). The same could be done for "phase technology" by the vasari, as they usually have a large margin of superiority over the tec and the advent, that there might be some base "phase mineral" that is required to be replaced in order to continue using the phase technology, meaning not just weapons, but also the phase jump technology and the phase out protection that many of their craft use.
In my mind what your idea, and my suggestions to carry that forward to other items in the game as well does, is make the game have more "events" to deal with, not just enemy fleets, or weapon numbers, and thus makes the game more interesting!!
Wouldnt it be cool, to have a small advent fleet cut off from their home planet making a run from a large vasari enemy fleet run into a planet where the tec have 20 marza's waiting, only to discover that the marza's are out of ammunition, and are forced to either ignore the advent, or to ram them in an effort to disable them. And what if the tec attack a planet in line with the advancing vasari fleet? Only to have that fleet now have limited ammunition and facing not only a sizable reinforcement from the tec on one side, but the homefleet of the advent coming to the rescue?
Haha, it sounds wonderful to me!!! What it does is make the game more interesting, and if it is interesting then to be honest i dont care how long a game takes. Do you remember going through the levels in Diablo and spending hours trying to get the loot and not die at the hands of the skeletons or the goblins? Haha, i used to spend hours and hours, until my parents of course said too much is too much, but my meaning is, that it was interesting, and therefor i was caught up in it, and enjoying every minute.
Keep the suggestions coming as far as i am concerned, not everyone will agree, but you know what, if the devs had toggles for things like this, those of us that wanted them could have them, and relish them, and those that didnt could decide to leave the toggle off.
Anyway, that is my opinion of your cool idea, and my small suggestions to go along with it. Hope you like it, and I hope, though of course i have no idea if the devs will even consider it. But to my mind, it makes it more interesting, and that is a big big thing. 
Sincerely,
-Teal