I feel ANY little thing you do to a bait changes its performance to some extent. The smaller the bait, the more change you are introducing compared to a large bait when you topcoat it. That said, lots of repaints are topcoated with epoxy and still work great so all you can really do is try it and see. I like to use a thin factory-like topcoat on repainted lures - my choice is Dick Nite S81 moisture cured urethane. One dip is as thin as a factory topcoat and very tough and glossy. But the stuff is not cheap and is hard to store without "going off".
I don't know how thick you make your Etex on musky lures. I've seen some beautiful ones with VERY thick topcoats but I don't think that would be appropriate on a small walleye bait for the very reason you're concerned about. Etex is relatively thin compared to other epoxies so I'd plan on a couple of coats, just enough to obtain a uniform gloss. Epoxies are only slightly more dense than water so you'd probably be OK. I wouldn't thin it. JMHO