As for which plastics do and don't leach; you might want to read this:
Plastic Bottles: Are They Safe & What Do The Numbers Mean?
(LDPE, and HDPE are actually
good choices

)
The biggest detriment (in
my mind), of using plastic in an ultrasonic cleaner, is loss of efficiency. UCs basically create very high frequency sound waves (or vibrations). Plastic bottles absorb those vibrations and make them less effective.
My cheap little Harbor Freight UC came with instructions, that stated using the hard plastic basket (included for delicate items; like jewelry), would diminish efficiency by up to 33%. I would
guess that the softer plastic used in a lot of e-liquid bottle would absorb even more.
Glass on the other hand, is quite rigid, and therefore transfers the sound waves quite efficiently.