Roundcube if InnoDB is enabled uses this engine, if disabled and it detects it perfectly, it uses MyISAM. Note, if you want to switch Roundcube from one engine to another, you'll need completely destroy da_roundcube and run ./build roundcube. As for directadmin related software that is all, and you should rely on your needs and requirements of used software. As I know that some CMS and e-shop scripts require InnoDB engine enabled. I personaly prefer not to use InnoDB, as it seems to me to be more fragile, than MyISAM.