Yes, the inside the windshield transponders are fine on the motorcycle. (generally much smaller than the license plate ones) They are sealed in most cases. Most people mount them on the back of the windscreen, down low where it's not in your line of sight. I use Dual-Lock, and several transponders come with strips of dual-lock for that purpose. I have in some cases drilled a couple of holes and run a zip tie thru and around the pass to prevent loss on off road rides or slow theft. I have multiple passes at the moment, an I=Pass which is all EZ-Pass locations from Illinois and also required no deposit, plus they charge no fees if you are not using it. I've had a static balance for years sometimes, then used it and zero issues. I also have a Pike Pass from OK that works in OK and for the TX pass sites like Dallas and North TX tollways.
If I was going to get an EZ Pass transponder now, I'd probably get a NC Quick Pass which is good in all EZ Pass states, and in FL and GA as well as NC. Might some day soon be good in TX and OK too.