I find that when I feed mostly flakes, with only some frozen, they lay better with better babies. Exclusive Mysis is really terrible with very poor hatch rate and deformed babies.
When I was breeding ocellaris, percula and clarkii large scale I was primarily feeding frozen Mysis (locally caught by myself), squid and feeder shrimp (all my pairs were fully grown except maybe for the clarkii).
I noticed that the eggs where usually rather clear, but I had hatch rates of 99% and usually only minimal losses during the first 2 months. Misbars were not overly frequent and deformations were usually minimal (still too much for my taste).
So I can't confirm that Mysis is generally bad.
The best available foods are of course pods: Calanus, Cyclops, reef plankton,... and of course live tigger pods. It's about as close as you can get to what clownfish eat in the wild.
Unfortunately these are usually expensive and it is quite difficult to get them sufficiently filled up with those. You would ideally have to feed them all day long in small portions. I try to feed it as often as possible, but Mysis is usually more convenient.
In general I found Mysis to be a good base food and you should be fine if you supplement it with some of the above and maybe some high quality dry food (flakes or pellets).
The issue with the Mysis we can buy is that they are all freshwater species. Alive they are pretty much clear and likely lack some of the nutrients saltwater Mysis have.
Back in Germany I also caught saltwater Mysis which are a whole different animal: larger and usually greenish or brownish from all the algae they consume. Unfortunately they don't form the massive swarms that make catching freshwater Mysis so easy and efficient. I was able to catch a years worth of fresh-/brackish water Mysis in 2 to 3 hours - and I was feeding about a pound (= 500 g) a week.
Of saltwater Mysis I was lucky to catch 100 grams worth during a whole day. These guys live in small groups among algae. I don't know if they form large swarms as well at some point in time - if they do I never found those.