When you edit the extension page on Extension Wahrehouse, you can increment the version number. I believe this should notify the user even if it is a listing page, but I have not tried.
Your extension will only be encrypted if someone encrypts it. Extension Warehouse does it for extensions that are uploaded there, but if it is hosted on your website, EWH is not involved and it is logically not encrypted automatically. There used to exist an official SketchUp Ruby Scrambler that you could use, but giving away encryption software will always enable attackers to crack it. So the scrambler only makes it harder to read your source code but does not prevent it because a cracked “unscrambler” exists already out there on the internet.
Why not upload the extension to Extension Warehouse and save your users some additional steps and confusion?