I've updated the Rules page to include explicit rules about sock puppet accounts. The gist is: bots are allowed, but using a secondary account to evade a ban is not. There are constraints on what bot accounts can do: they can't flag or leave user feedback. Furthermore, sharing accounts is not permitted.
These rules were added because people were using sock puppet accounts to evade bans. If they were just being used to passively use the site it wouldn't have been a problem, but some users have started harassing other users with these sock puppet accounts and that is definitely not okay.
You can see the exact diff here