In most cases, I vac around the rocks. I do have some rocks that aren't part of the main "structure" that I will remove and vac. Only once have I removed all the rock but that was to rescape. I will probably do it again soon when I try to sex the fish and cull back to a better m-f ratio.
As all my rocks are hollow and sectional (10 in all) I remove them all.
I remove all but 2 which I leave at one end of the tank. I vac then move the 2 rocks down the other end then finish the vac.
Each rock I empty into a vessel to check for fry (and hiding fish).
I then replace the rock in a completely different formation each time.
The fish then spend the next several hours re-establishing their patch.
Been doing it for 10 years this way without incident
I find by re-scaping at each water change stops territories being established so much which suppresses aggression/stress. I feel also by the way the fish 'have a go' at my hands it keeps them entertained.
I take about 5-10 gallons out of the tank and stir the whole thing up and try and catch as much debris as I can with the siphon.
Then I refill it with the garden hose (tank next to the window
) and try and blow out all the tight spots, assuming my fish haven't spawned. I pick up the rest of the debris next water change. I normally blow out the crevices every other change so its not so dirty or if my fish have spawned, I just wait till my nitrates get out of range.
Edit: You aren't going to get ich from a dirty tank, you might get septicemia or fin rot in really really bad tanks. You are only going to get ich my introducing something into your tank that is carrying the parasite. Quarantine your new arrivals for 2-4 weeks, which is enough time so any ailment will show itself. As far as freshwater diseases go, ich is easy to get rid of (I use copper in tanks with no inverts), it's salt water ich that is a nightmare.