It might be fun and in keeping with Traveller's "you don't always get what you want" philosophy to take a cue from the Heavy Gear construction system - after you finish a new design (or even a new ship) roll to see what defects show up on the shakedown cruise. Some things you will be able to live with, some that are critical to fix (and so your ship costs more) and some that you would like to fix, but are design flaws.
I would give "standard" designs some DM on the roll that would prevent the "you can't fix it'" problems, and the better shipyards won't build in obvious problems (that is, you get another DM based on shipyard skill).
For custom designs, the Effect of the Architect's " will go in to the roll. (Don't let the players know the effect - if they are suspicious or overly cautious, they can hire another architect to double-check the work, but at an additional cost of course.)
The sorts of problems I have in mind, in order of increasing seriousness
Design Flaws (require a major refit to correct)
Cramped hallway(s) (RP possibilities)
Bad lighting or security camera coverage in certain areas
Hard to reach maintenance panels
Inefficient Fuel Scooping in a Gas Giant due to poor scoop aerodynamics
Turret arcs obstructed by the hull
Poor Aerodynamics or Cargo Hatch design
Drives can't operate at full efficiency
Construction Flaws (come from bad shipyards and can usually be repaired with the right parts and money)
Strange noises
"Bad Wiring" for internal sensors (false warning lights, etc.)
Cheap bridge control interfaces that require upkeep
Faulty systems (enviro, floor grav, etc.)
Airlocks take too long to cycle or don't form a solid seal when docking
...
Drives that won't respond under certain circumstances
Very slow leak in the hull that doesn't become obvious for a few days (usually by the time you're in J-Space, hehe)
Just some ideas. A more clever person than me could no doubt come up with a fantastic table or three for this sort of thing. (John Brazer, are you listening?

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