As a LAMP developer, one thing that becomes a habit is using Innodb. For most websites. Innodb performs better, especially as simultaneous traffic increases.
However, Innodb comes at a cost. When I checked memory usage, MySQL was tieing up over 250Mb - over half the memory available!
Disabling Innodb dropped that usage down to 50Mb. Considering that most use cases of a BeagleBone as a server won’t need to handle thousands of simultaneous connections, I can’t see much downside to disabling it.