Aye, that would be a problem but Think of it in a tiered system.
Faulty engines:
Tier 1: -10% in battle flight speed, -1 to hyperspace speed
Tier 2: -25% in battle flight speed, -1 to hyperspace speed
Tier 3: -50% in battle flight speed, -2 to hyperspace speed
This one could get worse simply by flying, so if you take the first iteration sure it's not that bad, but if it grows to 2 or 3 you have a bad problem (slow fleet)
Compromised hull:
Tier 1: -10% hull, -10% flux regen
Tier 2: -15% hull, -15% flux regen and dissipation
Tier 3: -30% hull, -20% ALL flux stats and a small chance to randomly blow up
This one can have things like: reduced cargo, reduced fuel, reduced etc. Even going to 5 or more tiers when getting creative. I think it should grow as you take hull damage (even out of combat hull damage)
Glitchy sensor package/
Tier 1: +5% sensor profile -5% sensor range
Tier 2: +5% sensor profile, -10% sensor range, +5% cost to scan things
Tier 3: +10% sensor profile, -20% sensor range, -5% to all ships sensor range in fleet, +5% cost to scan things, and +5% jump time (assuming SS ties FTL navigation through sensors)
I think the best way to increase tiers would be simply being scanned or scanning (so using that ships sensor package) there could even be higher tiers where if the ship has a small chance to make your fleet see the wrong thing (so you see a sensor of pirates but it's actually hegemony)
There are tons of ways to move on that system, obviously numbers should be edited, but you should have tier 1's be alright to have (in some cases) while higher tiers get harder to justify having (and making top tiers bring about a decision to sell the ship or fix it). It would also tie nicely into people wanting to pay hard prices for fixing ships, and it should cost less for lower tier and fewer d-mods (do you fix it now for a reduced price and hope you don't need money later, or cross your fingers and hope it doesn't get worse?) I think it would add interesting player decisions to the system and a depth to it (also it could have the way for new d-mods).
This could add dynamics like:
Get in a fight with a high tech faction and see a really rare ship, so you could use ion weapons to disable it (forcing you to invest crew or Marines to get it) or use some sort of crew killing weapon, these things take time so while your circling this high tech ship doing minimal damage and trying not to give it d-mods your fleet is fighting, Is the prize worth it? The possibilities!