Using destroyers to flank is entirely appropriate. Bear in mind that they'll need a fair amount of PD in late-game to deal with fighter-heavy Bounties.
BTW, the whole "11-ship" rule means that you're penalized actively for setting the Battle Size too high; the enemy will have a huge numbers disparity (but, if you've been careful about picking Captain perks, you'll have a lot more quality; all those stacking bonuses really matter). Unfortunately, that also means that you get into trouble with CR, simply because clearing each enemy "wave" takes a while, even if you can do it easily.
This is one of the reasons why I've disabled that rule (only 10 Captains) in my personal mod, and allow Captains to hit Level 29 (essentially, allowing them to max out their skill bar), so that late-game battles aren't a massive drag or flat-out impossible if the enemy brings enough numbers.