I clean optics a lot in my day job. Any optical surface will get a grubby coating with time, almost anywhere it is used or stored. Some places are obviously much better than others, but the air is never completely clean - none of us print in a clean room. Many camera lenses have an age film on them, the owners just haven't noticed! It is much more noticeable on optics where you shine light through the lens - such as enlargers and projectors. The best way to show up grime is with one of those LED torches, a single blue LED seems to be the best. Shine one of these through a lens in a dark room and look through from the other side. It shows up the dirt extrememly well and it is often possible to work out which surfaces it is on, too.
As for storage, I think the biggest problem with fungus is humidity. Not sure of all the ins and outs (not being a mycologist!) I just know that equipment sold to India seemed to have a lot of trouble with fungus (hot and humid)... Maybe an airing cuphoard might be a bad idea.
The biggest problem with cleaning optics is scratching the lens. For this reason I don't like rubbing with a dry cloth or tissue. A lens should be cleaned wet - wash rather than scrub - and make sure you blow any loose matter off with a brush, first. I prefer to use hand wound cotton wool buds (on a wodden shaft) and a solvent. It is difficult to get decent solvents, these days, due to health and safety and anti-terrorist legislation. Pure ethanol might be the best you can do, although it isn't really volatile enough. Petroleum Benzine (also called Petroleum Naptha) is good, but it really needs to be pure reagent grade. It is basically lighter fluid - but the stuff in the tin can sometimes be a bit oily, which isn't helpful... Most lens cleaning fluids are demineralized water with a dab of detergent and a few percent of ethanol. They don't do any harm, but they aren't much good at cleaning, either...
Acetone is a good lens cleaner - but it is even better at seperating balsam (real or synthetic), dissolving paint and damaging lens mounts. Don't even think about it!
Just my humble thoughts...