I think I have two comments. First, on predictability, and second, on fun.
1. A fleet admiral should be able to sit down and know what to expect if he loads his ships too heavy. The consequences of running without enough supplies are predicable (no repairs, right?) and the consequences of running with too many supplies should be reasonably predicable, too. Lower speed, maneuverability, extra fuel use are predictable. Having extra cargo cause your ballistic weapons to be less effective, for example, is not at all predictable.
2. Due to a variety of psychological factors, human beings do a bad job planning for random low-probability, high-impact events. As such, rare but huge accidents, like losing a whole ship, are just not going to be fun. It can be totally justified, it can be realistic, and it can be the player's own fault, but it's never going to make your average player happy. Unless by "ship" you mean "a fighter or two out of a squadron", I'd drop it. There's a really high risk it'll be unfun, even though it's a "consequence" of a player's decision. I'm certainly willing to be proven wrong in playtesting, though...
Just my 2 cents.
One question: Why wouldn't everyone run their ships at 149% all the time? There probably should be some minor, predictable, consequences.