One thing I didn't mention when I posted about cleaning the Torah scrolls is that the sofer who told our Rabbi how to clean them also recommended airing the scrolls on a regular basis. Again, something we'd never thought to do. The Rabbi says the sofer literally unrolled the Torah out on a long table (we had 4-5 8' tables end to end for this project (two sets, one for each of our scrolls)) then brought the end of it up to fold the scroll over itself so it was sticking up in the air.
He recommended leaving it for a couple of hours before re-rolling, and doing this regularly so that each part of the scroll gets a chance to air over the course of a year. (I do not know what the recommendation is for how many times a year each section gets to air.)
The logistics of this can be easy or really hard depending on if you have access during the week or during non-service hours on Shabbat, what space you have to unroll the Torah, security, etc.
My guess is that even allowing a rolled up scroll to be out (I'd try to stand it up if possible...maybe even build a stand to do this) in the main room without the cover will help air it.
You might consider different covers too. If the cloth is thick or made of synthetic fiber, it won't breathe as well. Also be sure to change covers and wash them (if possible). For example, we do this once a year at our shul, as we have a special High Holy Days cover.
There are no sprays. That's something I can attest to as I do a lot of work helping people with chemical sensitivity and mold sensitivity overlaps strongly. You can cover up the smell but you can get rid of the underlying problem (and it is something that can damage the scroll so you really don't want to just cover it up).
If there is mold in the ark itself, then yeah, you have to deal with it. The best way to get rid of mold is to physically remove it. So wiping. Use a basic cleaner (I'm a fan of Biokleen as it's natural, doesn't leave lingering scent, and really works) and lots of rags. Is there carpet or other fabric on the floor/walls/ceiling of the ark? Or curtains? I'd consider completely replacing it (or at least removing and washing, if possible).
You might think using bleach will kill mold, and it can to some degree, but studies show that plain white vinegar works even better. Make sure not to leave water/dampness. Wipe down the inside of the ark with vinegar after cleaning (don't forget the inside of the doors). Let air very very well.
I'd also recommend ozone, if you have access to a machine. It does require electricity so I hear you that this is maybe not possible. But it would be a one or two-time thing for a few hours. Never run it when people are present. Run in the empty ark for a couple of hours then turn it off (while holding your breath) and air everything for another couple of hours. Ozone does not kill mold but it will oxidize some of the byproducts of mold that can cause damage/smell/health issues. You can ozone the scrolls themselves but ozone oxidizes whatever it touches (like the inside of your lungs). A small amount is unlikely to damage anything but, with scrolls that might be hundreds of years old, I wouldn't recommend taking the risk. But if you have an unwashable cover that isn't an antique, you could ozone that.
There are materials that suck up moisture (like the little silica packets in vitamin bottles) that you could place in the ark. I know there are versions made for spaces that size. You'd have to replace or recharge (remove moisture in an oven or the sun) periodically, but this could be an affordable no-electricity help to reduce humidity levels, though I'd research them to see how well they work in your climate and situation.
I would very much like to hear what does and doesn't work for you.
