Red - I see a little bit of misinformation in your post... please don't take offense to what I'm gonna say. As far as I can tell, "completely" cleaning out your tank doesn't mean taking everything out and scrubbing it. From what I understand, dom418 just wants to know if we bother moving rocks around to get at gravel that hasn't been vaccumed. Regular gravel vacs will not destroy your bacterial colonies. Trust me on this one... once the colonies are established, they are extremely difficult to remove by physical means. Take a look at fluidized bed filters. Basically a continuous dust storm contained in a tube. Bacteria has no problems clinging onto the sand particles in there. Before I got into cichlids I used to do complete gravel vacs once a week on my tanks. I never had problems with mini-cycles occuring. Many ppl here will also tell you that they gravel vac as much as they can. On top of that, if your tank has good filtration, most of your bacterial colonies will resign in your filter(s). So even killing part of your bacterial colony in your substrate/decor won't hurt your tank. One more thing, in an established tank, you should never ever see nitrites present in the water. That means either your biological filters have crashed, you dumped a load of food in your tank (in which case ammonia would be present as well), you put too many fish in there all at once, a combination of all of the above, etc. etc..
Now that I have a Lake Malawi tank (with tons of rock work) I usually only vacuum the gravel that I can easily access. Every once in awhile if I have loads of time and am not feeling particularly lazy, I'll take apart some of the rockwork to vacuum up the gravel there. Needless to say, I'm somewhat of a lazy person, so I don't do it often.
HTH
-Richer