Not as far as I know, so long as you use the correct ones. It can be tricky to get the correct console command that doesn't break other things. Like a common reset is setting the npc to "never met before" dialogue trees. But if they are a point of contact for a number of quests, that might be a very big problem. I would highly recommend checking out one of the various wikia pages to make sure you get the correct fix to any broken quests. The TES/Fallout communities have always been very good at finding the optimum solutions for Bethesda's bugs.

Cheating via console commands is no big deal. Steam doesn't even recognize you're doing it in regards to steam achievements.

It was something I occasionally had to use in Fallout 3/NV, specifically the dumping quest items taking up inventory space. That was before Bethesda patched NV so most of the quest items ended up with zero weight.