1. Nope. The eggs'll be fertilised if the males and females are together, but that won't affect the taste or condition of the eggs (unless you allow them to sit in hot weather for a few days, of course.)
2. If you mix Muscovy and either of the other two breeds, the offspring will be sterile. If you breed a male muscovy to female mallard-type ducks, the offspring will be mullards, and will not lay eggs, but have very good weight gain. If you breed a male mallard-type drake to a female muscovy, the offspring will all be hinnies, and will lay eggs (or so I've heard.) But runners and Pekins are the same species, so they can interbreed without problems.
EDT: the offspring from both crosses can be either male or female. Male mallard x muscovy should produce some small males that will not lay eggs. Sorry, I just realised how unclear my post is.
For egg production, I'd go with runners. Pekins are calmer, but they lay fewer eggs. Muscovies lay eggs pretty seasonally and attempt to build up a clutch to brood. When they're brooding on eggs (35 days or longer) they won't lay any more eggs.
Be careful about your duck to drake ratio. Drakes are fine fertilising seven females or more. (That's the ratio I had this spring, and every egg hatched, except those that were killed by the high humidity.) but drakes are really hard on ducks, so you don't want more than one drake for every four females, and fewer drakes than that is better.
If you choose to mix breeds, it's best to put lighter drakes with heavier hens. I would not have a heavy Pekin with little runners, for instance.