What is the exact error message of the 500er errors on the websites? You will find these errors in the error.log of the site where the error was displayed.
I needed help figuring out why I can only enable 1 SSL site
you can have as many ssl sites on a server as IP addresses are assigned to that server. thats a limitation of the ssl pürotocol and not specific to ispconfig. Just ensure that you select a dediacted IP for every site that shall have ssl enabled.
Regarding the probing of your server, thats normal and happens to every server that is connected to the internet all day long. So nothing to worry about. Just ensure that you keep your server updated and that you also run up to date versions of the cms systems that you have installed in your websites.