Yes, they are still in the matrix

will they ever get out? I guess we'll have to see in a future comic.

Comic transcript

Panel 1:
Rasta Pigeon, is looking at a lemon squirrel.
RP: So, we wanted to get rid of the lemon squirrels, put them in the matrix ...
Panel 2:
RP: ... and then followed them in?
Lemon Squirrel Neo and Lemon Squirrel Morpheus hop by.
Panel 3:
P: Yeah, if you put it that way, that is kind of stupid.
Many Lemon Squirrel Agent Smiths hop by.