I realize that only devs with gamma know the answers, but these are only half questions/half musings over potential secondary effects of upkeep.
We can safely assume that upkeep will be deducted from incoming planetary income. But how about other sources of income?
What about credits made on the Black Market? If we control a sufficiently huge number of worlds and asteroids the amount of money made buying/selling on the Black Market could be notable, if it is unaffected by upkeep then resource markets could be even more useful lategame.
What about trade ships and trade centers? I suppose that if we are taxing money from the planet populations we will surely be taxing the orbiting trade centers too. But again, if it turns out they are unaffected then they could become even more vital for maintaining lategame economies (and become more important assets to guard/attack).
Last I heard there are also a few abilities ingame which can generate currency. Like the Sova's Embargo, which steals income if in a local hostile system. Will upkeep penalties be applied to this too? If not then yet again we have an ability which will become more useful as our empire size grows.
There are probably other ways to scrape up some credits ingame that I am missing. Having an ally in a lower tax bracket give you credits, perhaps there are ecomony affecting artifacts, maybe selling/scuttling structures (do they give credit/resources back? I dunno).
I am sure the majority of our credits will be made from planets, so upkeep will hit us hard, but if planets are in fact the -only- things hit with upkeep... well it certainly makes for some interesting dynamics in other lategame money making tactics.