Fleet supply is an inevitable choke / slowdown on your economy except on larger maps. But I find (at least in SP) bad things come from not moving up in fleet strength in the later parts of the game. On the other hand as Greg pointed, some throttling with careful choice of units used is quite useful in the earlier parts of the game after your initial expansion wave and before you can start the wholesale invasions of your neighbors. On cruel SP games, counter-attacking a scouted gravity well after fending off a mega battle at your SB + defenses is also very useful. As in all thing timing is key.
On the contrary if you are running out of funds early to mid-game you might want to cut back on your research even further. Also while useful don't fall in love with the black market. Try to sell to the AIs, don't accept the cruddy bargain prices for whichever resource you have a glut of. If you need to dump on the market try to trigger when the price is good.
Also culture is key for extractor rates and even more key for advent, don't neglect it. I usually run out of money / resources when I hit a new key ship prototype and I have scouted my enemy and it is time to get the next leg up on my fleet.
Again in cruel AI games, my focus is on the chokepoints and how to secure them with fleet / SB / defenses and key tech. When I get a breather I fill in all my ice / volcano worlds. I mean if you can't afford the pop infrastructure upgrades, don't need the logistics slots, and don't yet have trade researched why kill yourself with planets that will sap you with under-development taxes. Trade as soon as you can is great but on some maps at higher AI levels if you go trade to early you die, pure and simple.
