If you use silicone, be sure it is some variety that is safe for aquarium use (don't want anything with anti mold additives as they can be bad for fish.) Be sure to let it cure for the recommended length of time and such since the fumes are nasty.
I usually use PVC cement for gluing PVC pipe where it is under pressure or likely to get knocked about and be in danger of coming apart.
I have occasionally used some silicone for low/no pressure drain piping to keep it from leaking where I wanted it to be easy to take them apart later. I'm not very patient though and silicone requires a fair bit of time to dry properly. PVC cement cures very quickly.
As to gluing rocks..... I've never glued rocks. I know there is a black polyurethane foam that has been used for securing rocks in
pond waterfalls but I've always just arranged rocks so they will stay put.
I will warn that a waterfall may tend to cause a lot of splashing and water loss and might not be all that desirable indoors. Humidity could be an issue and the more splashing there is, the more evaporation is likely to happen. Just something to take into account in your planning.