The messages plugin now contains IM and mails, of course it became heavier as it is more complicated feature right now and consumes more server resources then before, let alone the fact that you have shared hosting with total 500 users and 10 users online. I believe anyone will tell you that shared account is no good when you have 10 users online.
Anyway, if you provide us with access details to your server and website, we would like to test, what exactly is causing such a big load on the server.