In that way it doesn't, IMHO, negatively affect the game. It adds a bit of mystery and challenge to otherwise "jaded" players.
That being said, I would in all likelihood, NEVER allow a players ship to deviate from a standard canon design. This would bias the game and I simply think it stops being Traveller if nothing in canon is there to put a limit to work around.
Oh, let them play with a design, even the Annic Nova, but when breakdowns occur there isn't a local garage that can fix the mounting problems.
Before long, they'll be abandoning, or trading in, a derelict and acquiring a more standard ship.