I'm paranoid and dealing with my first loaches. Any insight would be welcome.
3 weeks ago I purchased 3 Botia kubotai http://www.loaches.com/species-index/botia-kubotai an put them in a 10 gallon QT tank. They only stayed there for a week, 5 days to be exact, and I went ahead and put them in my 46 gallon tank. Yea, way to short a QT but ...

While they were in QT I noticed 2 liked to hang around each other while one always liked to hide in my cave.
Fast forward to today.
They are living in a 6 month old 46 gallon bowfront with Corys, Neon Rainbows, a female ram, a Betta, and some rasbora. The tank is moderately planted, borderline heavy. My nitrates typically drop to 0. I try to do weekly 50% water changes and get there most weeks. Ammonia and nitrites are 0, checked weekly now.
Nightly, and in the morning, I see 2 of my loaches playing around, eating what's left of the snails, and doing the up and down dance on the glass. I haven't seen the third loach in days.

They live in a plastic stump with a hole halfway up. A nice hiding place without any sharp edges to get hurt on.
Should I assume the worst, or are some loaches so shy they only come out late at night? If he's dead in there what should I expect to have happen? A rise in water pollution? Right now it's crystal clear.
I'll end this with a photo of the tank. The loach motel is the stump thingy on the left.
