Mine is a 20L with 1/8" plexiglass. Pure silicon caulk is fine, so long as it doesn't contain any mildew inhibiting agents, or other additives. It doesn't bond readily with plexiglass, but if you sand the sides and rough it up a bit, it does ok.
FWIW, if I had to to it over again, I would probably use glass, as cutting the plexi was a bit of a pain, and the 1/8" while cheap, does flex a bit with water running through the sump - if you go plexiglass I would use 1/4".