Dominions had Ermor and Warlords Battlecry 3 had undead but I can't recall anything about their upkeep. TW:Warhammer had a strong bonus from magic universities, especially named ones.
Ermor (or, well, the undead passively murderous ermors) is kinda' interesting on that front, in that while their unique units themselves don't, strictly speaking, have upkeep in terms of gold or supply, they do have upfront costs (of different sorts; the major casters cost death gems, everything else requires some degree of infrastructure, albeit the absolute most basic of its stuff only requires dominion) and they're actually one of the more logistics
limited factions in the game.
Infrastructure and logistics is far and away one of their greatest weaknesses, because they're very dependent on both death gems (which requires conquest and holding specific areas) and gold (to build temples and castles, to enable more and better passive undead generation), the income for which their very nature rots out from under them. Plus one of their stronger advantages (the massive hordes of undead) is pretty difficult to concentrate and move around
and requires construction to really get going. It makes for a necessarily aggressive playstyle that's simultaneously pretty unwieldy and easy to kneecap on the logistics front -- hands down one of the most thematic "undead apocalypse" implementations in gaming, but the exact opposite of one that emphasizes a reduced reliance on logistics, heh.
There are two series that come to mind that do something rather interesting in this field-- in one, a guy is in a 4X-based world, fighting against an enemy from a turn-based RPG world...
That sounds kinda' interesting, happen to remember the name of it? Maybe the other, too?