Is it against SE rules or suggested good practice to have a different profiles for every SE site rather than a single profile?
Managing more than one login is a utter and complete pain (and I have a second account for a reason, and I only use it at work), and there's no real benefit from it.
Having one per site means separate emails and passwords per site
If you have a separate account per site, in theory, they won't interact with each other but there's a reason we have a single sign on across the network.
This might also lead to some weirdness if you do accidentally create a second account on a site you do already have another account on, especially if you manage to trigger off an automatic account merge. (It shouldn't happen.) You would also run afowl the rules if you're suspended somewhere and accidentally interact on another account.
Save yourself the pain and make use of the mostly excellent single sign on across the network.
Yes, if you want to have separate profiles per site you can do it that way if you really really want to since those profiles won't be able to interact with each other, but there are significant advantages to having a single profile.
You can benefit from the association bonus on all sites. This means, amongst other things that you start out being able to comment on any site you join.
You also see all messages in one place e.g. if someone comments on one of your posts, you'll see that message regardless of which site that comment is posted on. Otherwise you'd have to log in separately to each site to see if anyone's asked you for clarification or in fact solved your problem.
You can always hide your profile on some sites so it's difficult for casual viewers to see that you're active on particular sites if you're worried about your privacy.