Q:

Why has seahorse-plugins been removed? 

I've been encrypting and decrypting files and folder using nautilus and the seahorse-plugins package for the past few Ubuntu releases.  It appears that seahorse-plugins is no longer available in oneiric's repos: see here, and here. 
Has it been replaced by another tool? 

A:

Looking a bit further there is this bug report #796752 on Launchpad which seems to lay the blame on the transition to Gnome 3.  Looks like it might be available in Precise.