This will not be a cannonical answer but just some of my experiences. A real archivist can give you a fuller answer.
Paper is a tricky medium, whether you are storing maps or have a library of books. The problems of degeneration are compounded for maps because climate can not only causes the paper to degenerate but can also cause the paper to deform (warp, shrink, ripple, crease, expamd etc) which will cause your maps to become inaccurate. So, for paper, scan as soon as possible and if you need a hard copy, transfer to mylar asap as a back-up and digitize from the mylar. Handle the paper as little as possible and do not store in wooden cabinets (the acidity will damage the paper). Lignin-based storage for lignin-based map-substratess = FAIL (eventually - it takes a few years!).
'Nuff said! You need never handle the original again (with luck) and it is handling that does 99% of the damage.
This is the traditional material and we had loads of paper maps copied to the stuff. However, it is not perfect either. We stored ours in vertical metal mapchests, this is better than lying flat (I'm told) BUT, re-inforce the holes where the maps go on the hangers. Our chests were like giant multi-hole lever-arch files. With much handling, the holes will rip, maps will fall to the bottom of the chest and even mylar can crease, tear etc.
Pencil, ink etc:
It all fades, especially on paper. The old adage of store in a cool dark place is as good as it gets.
Hang, lie flat, roll or fold:
Um.. well the order above was our order of preference and also reflects the decreasing space requirements (because with hanging chests you can't store stuff on top up to the ceiling).
How often did I enter the map store and confidently drag the ladder to the most dusty distant corner (because that's where the maps SHOULD have been) only to scrabble and swear my way through the store for an hour until I found the map in some random location? Look and learn! Document everything, become psychotic about checking in and out, become certifiably retentive about categorising and arranging your storage. Everybody will hate you, but they will find their maps quickly without damaging other items during their search. It sounds like you have a big storage task. So, get a librarian or professional archivist (even if only part-time). That's what they are trained to do - catalog stuff! You won't regret it. Also, computerize the catalog.
Paper cuts = blood = dull red stains on the edges of paper maps = you can't sell those ones (our problem, though yours sounds less severe).
This comes under your "anything else" category. Sprinklers will kill your maps as fast as the fire you're trying to put out. Metal chests are not necessarily the best answer (surprisingly - because they transmit the heat inside and stuff can still burn). Wood can burn sacrificially - but see the issue about lignin above... so... I don't know what the answer is because it sounds like a Catch 22. I'd go with metal, concrete floors and ceilings, climate control, no windows and double fire doors if your collection is THAT important, otherwise just accept the fact that you can't afford it, get the best you can and have digital copies somewhere off-site.
Not sure what you mean here but we used to sell a lot of our stored maps. This means a lot of traffic in the map store and a lot of handling. Think about ergonomics of lifting large flat sheets of paper of high shelves when up a ladder, without ripping them... now consider what level of wastage you are prepared to accept, because it is inevitable if that's your storage system (see 'blood').
Purpose of map:
Well... common sense can help a LOT here. Store the high-use stuff in multiple copies near the door. Reserve the top-shelves and back-corners for the less-used stuff. Traffic through your store = damage + hot steamy/sweaty bodies with sticky fingers. Limit the potential for damage.
I'm running out of my empricial observations.