Most of us will be sending manuscripts to agents first I suspect, not publishers. But either way I'd ask them what they want. In the old days Helvetica double spaced seemed the way to go. But a lot will now read the first part of an MS on an ereader so that may be irrelevant. I deliver my books electronically so it's pretty much irrelevant there - I just deliver in the form I write, 12pt standard font, 1.5 line spacing, and let people change if they wish, for an ereader or printout.

So ask - they'll be happy to tell you. I'd never print out anything justified - doesn't work on a big page. Can't imagine why anyone would refuse to read something with proportional fonts either. But it's a book manuscript not an exercise in desktop publishing, so forget about 'design'.