Can Macbook be serviced by Apple Care with FileVault enabled?
Firstly, I think this would be better handled by calling Apple Support directly. I do not see mention of this in any of the repair terms and conditions documents on apple.com.

Secondly, regardless of whether Apple requires FileVault 2 to be disabled or not, I would recommend that you follow the same process you did before - backup all the data, reformat it and install OS X afresh before giving it for repair. This would protect your privacy and also reduce (or prevent) wasting time with support if/when they inform you that they would have to format the drive and install OS X because it's encrypted with File Vault 2.