WHMCS really needs to be converted to innodb and use transactions so it's ACID (http://en.wikipedia.org/wiki/ACID). On numerous occasions (for a lot of different reasons) WHMCS has 'blow up' and then the database is left in an inconsistent state. The easiest example is that the invoice generation process blew up. You then end up with an invoice without all the invoice lines or an invoice with the header and all the lines but the next due date incorrect. If WHMCS used innodb and transactions anything that 'blew up' would get backed out and your database would be consistent and you could correct the issue and then re-process.
Yes, I do understand that this would be a huge change to WHMCS but something as important as a billing system needs to use proper transaction management.