Don't forget engine damage stuff that comes back slowly over time. Likely acid damage over time would process every time the ship is updated for the next tick which happens whether it takes acid damage or not, resulting in virtually no noticeable lag.
True, though I suspect the engine damage recovery stuff is just a +<engine health> per tick, and doesn't get treated as a hit, so it would be quite lightweight. On the other hand, Medic Frigates and Attritioners cause regen/degen on the fly and don't seem to be too bad, so it might not bog the game down. Will have to check them out when I get the chance and see what makes them tick.
Medic Frigates/Engineers repairing units are done differently than damage over time or self repairs.
The first is an external unit causing other units to be repaired, so the ability processes it's turn when the unit with the ability processes their turn. This means that one process has to scan and work on another unit which means finding the all the appropriate units and updating them. This does not mean they do not get their own turn, they get that on top of it.
The second places an effect on the receiving unit. The damage processes when the receiving unit takes it's turn. This means that it takes it's turn and during that time it takes the damage. It does not have to find the unit to affect since it is the unit affected, so the extra processing time is negligible and resolution is faster.
The game already has the former as you said. It can affect a lot of units at once with little performance problem. Because of that, the latter would be an almost trivial task, as a more complex task is already being accomplished without much impact.
Engine Damage repair, Armor damage repair, and the like are also examples of the second case, as well as units who construct their own modules, heal themselves (including vampirism), Damage themselves (including self-attrition), etc. Area attrition, Area speed reduction, area affect attacks, and the like are all examples of the former type and would be more difficult to resolve quickly.