I see some stored procedures in one database I'm managing that have the regular stored procedure icon, but with a little padlock next to them.
The differences I see is that I can't "modify" them, and if I try to script them, it says:
Text is Encrypted.
Is this because these are CLR stored procedures?
Are they "regular" procedures, but encrypted/protected somehow?
Is there any way to get to the code of those (either the T-SQL or the IL)?
The padlock means that the stored procedure has been encrypted using the WITH ENCRYPTION hint (see CREATE PROC in BOL for more information).
It doesn't mean that it's a CLR stored procedure.
Here's a SQL Server Magazine article on how to decrypt objects which are encrypted using the WITH ENCRYPTION hint.
There are also third party tools which do the same thing - native sproc encryption is not meant to be a strong level of encryption.
Edit: Here's another, but I haven't tested it on SQL Server 2005 or later.
As well as encrypted, it also means you don't have VIEW DEFINITION rights, so can't see the code of the stored procedure.