I realize this is an "ancient" thread, but I've recently come across this concern as well. I maintain several small databases amongst several servers, and WeBWork is the only software that still "requires" (per the documentation at least) MyISAM tables. I'm trying to unify backup solutions across the servers, but having these MyISAM tables is making this difficult.
Are there any "official" updates on the performance of InnoDB vs MyISAM with respect to serving a WeBWork database? I'm on Ubuntu Server 18.04 with MySQL Server 5.7, running WeBWork 2.13.