I like using a siphon to suck up any detritus on surfaces. Other than water changes and vacuuming I don't "demolish" my tank for a deep clean too often. Maybe once every 6 months? You don't want to harm the good bacteria!
Well honestly I rarely deep clean to that extent and don't really see much of a need to but my tanks also have very few ornaments and more plants so that helps. If you feel you need to clean the items in your tank what I would suggest is alternate which items you clean, much like being sure to never replace all the filter media at once, if you clean one this time you can clean another the next time.
However from what I understand the majority of the beneficial bacteria lives in the filter so you should be okay to clean however you wish but to be on the safe side you can alternate like I described above.
Also I am sure you know this but when cleaning be sure to never do a 100% water change unless it's needed to medicate a fish. I just wanted to add that in just in case you didn't know.