I investigate a little and found this bug on Ubuntu's LaunchPad:
https://bugs.launchpad.net/ubuntu/+source/faac/+bug/374900
The messages #14 and #15 are interesting. They mention an alternative that
seems to be free of licensing issues. It is called ffaac and described as
"ffmpeg's internal AAC encoder".
The first good news is HandBrake plans to "drop FAAC in favor of FF-AAC" :
https://trac.handbrake.fr/ticket/127
This alternative ( https://trac.handbrake.fr/changeset/4031 ) and another one
( https://trac.handbrake.fr/changeset/4029 ) seems already functional... but
faac is still used ( still according to
https://trac.handbrake.fr/changeset/4031 and to the status of
https://trac.handbrake.fr/ticket/127 ).
Would it be easy (like in editing the makefile and removing a directory) to
drop faac? Has it already been done by Trisquel? I do not know.