I do wish supply & logistics mattered more in computer space strategy games. I admit I'm not sure how realistic it is, but I do think it improves gameplay. It's probably not a coincidence that the few sci-fi titles I can think that boast any sort of supply/logistics element are also among the ones I've enjoyed the most.
Birth of the Federation's supply/logistics system is very basic, but it does have one. There are two main components:
1.) Your ships' range is limited by that of the nearest outpost, starbase, or shipyard (which can only be constructed in inhabited systems). Notable in that unlike a lot of space/sci-fi titles, ship range is short enough (even in the late game) that constructing additional shipyards & space stations is a necessity.
2.) The number of ships you can build simultaneously is limited by the number of dilithium sources you control (and is continent upon you having also constructed & powered dilithium mines to properly exploit them). This feature is marred, however, by the fact that the AI can build as many ships as it wants regardless of how many (or few) dilithium sources it owns.
While a deeply flawed game in other respects, Stardrive 2's possesses a nice, simple logistics system that works pretty well: :
Each ship type carries with it a certain amount of fuel; it can be increased with certain technologies and resources found the map, but it's always limited. Ships/fleets expend that fuel whenever it travels outside your owned sectors (the galaxy map is divided into sectors/hexes -- it's actually a pretty neat mechanic), but can refuel at any owned sector with a colony or space station. If a ship/fleet runs out of fuel, it automatically flies to the nearest refueling point...but at a crawl; it cannot deviate from this plodding course until it refuels. In this way, the player is encouraged to not send their ships too far out, and to keep colonies & space stations within a reasonable distance of each other.
Distant Worlds, of course, is pretty well-known for its supply & logistics model. It's pretty satisfying when that seemingly all-powerful empire bearing down on you with its mighty fleet suddenly stalls because it ran out of fuel (perhaps because you launched a daring raid on its main fueling station?). In an odd way, I also appreciate when my shipyards are backlogged on my queued production, due to a critical shortage of a certain metal (even if it's frustrating in-game); it's how I know the game isn't just magically still creating ships out of nothing.