Is there a way to encrypt the remote password for 3.11 or 3.12?

No. This was added to 4.1. To accomplish this in 4.1, do the following (this is also found in TID1001567):

LOAD REMOTE <password>
REMOTE ENCRYPT <password>

This will then give back the prompt on how to load remote and ask you if you want to add it to the LDREMOTE.NCF file. For exampe:

          To use this password use the command:
                 Load REMOTE -E BDC8DBBD8328222182

          Would you like this command written to SYS:SYSTEM\LDREMOTE.NCF? (y/n)

At this point you can do any of the following:
1) Add the line LOAD REMOTE -E BDC8DBBD8328222182 into the AUTOEXEC.NCF
2) Add the line LDREMOTE in the AUTOEXEC.NCF

The remote password is now encrypted.