1. Yes, you are able to later upgrade your s2Member account, under
My Account in s2Member.com, next to your avatar there is an upgrade button I believe, and you will only be charged the difference of price between the two licenses (the one you have and the one you want).
2. Yes, you are able to later change the domain in which the single-site license will work on. Under
My Account in s2Member.com, right above your avatar, there is an edit profile link, in there you just change your primary domain, which is going to be the only domain in which s2Member will work on a single-site license. This info is asked during the checkout.
3. Yes, s2Member Pro is encoded in two different flavors: ionCube® & Zend® Guard. I'm not sure if the free version is also encoded though. Check this post that has a lot of complete info on s2Member:
viewtopic.php?p=29120#p29120Hope this helps.