all ships shoud suffer from combat, including capitals, but not from fact of deployment, it does not matter how ship fly around.
frigates shoud go malfunction after some shots, capitals after prolonged fight (or large amount of encounters, this will be logical), hitech ships faster, lowtech slower.
ships will already damaged hull shoud drop CR ever faster (snowball effect)
such system will be clear to understand, since all values displayed in raw (not hidden behind percent and obscure game mechanics), player will know how much each action know and how much reserve each ship have.
if ship A have CR of 9000 (no damn 50% or 60%) and consumption rate of 100% (ships like hyperion will have large values, like 400% and lowtech capitals lower values) fire gun with CR consumption 100, it will have 90 shots (it still can shop after CR deplition, but with malfunctions), shared for all instanced of that gun (very logical, heat managment is severe problem for space ships)
soo it will be reasonable to install low CR cost guns on ships with hard maintenance (and heavy guns on ships with easy maintenance).
If shield damage count as 0.1 CR (shoud be shared for all ships, shield efficiency already present) - maximum possible damage soaked by shield will be 90000 at flux:damage 1 (hitech ships with flux:damage 0.5 will hold 180k without issues on same other rates) after that shield will go eventual malfunction (just like everything else).
system with clear digit indicated max CR and current CR and maximum CR as value, not percent, with all guns without ammo but with CR indication and clear supply cost per CR will return strategic element into game.
if ship have 9000 CR and cost 0.01 supply per CR, it shoud tell player exactly that value.