Military History Visualized of YouTube says that Naval strategy is a built strategy, and a country loses command of thr seas if its fleet is destroyed faster than it is built.
That applies to seas. Starsector is in space. While patrols are destroyed, we don't really know the true extend of faction reserves. Each and every navy always has something in reserve. You destroy some ships, they can replace them. Once the replacements are destroyed, then you can worry. However, this has nothing to do with the following:
Would open up gameplay opportunities and make game mechanic more intuitive if a colony’s fleet size is reduced whenever its patrol fleet loses ships,
Why should the numbers of population be influenced by ships losses? I could understand if that was an effect of famine or saturation bombardment, but otherwise it doesn't make much sense. Japan lost a huge majority of its navy mid-44, leaving it with a single fleet that never undertook a major operation again (if we discount the operation Ten-Go). However, they kept fighting until September 1945, and would have continued, should americans not have dropped nuclear bombs - but that's history fiction at that point.
My point is however, that losing the fleet didn't influence the combat spirit of japanese. They kept fighting, defending isles, and continuously fought wherever they were attacked, be it China, Burma, Pacific, or Indonesia. Civilian population, while under very bad situation, perservered - except for the ones killed by american bombing and its effects. Destroying navy shouldn't reduce the size of colonies, because it just doesn't influence it. If you manage to cut the supply of food or materiel to it, then sure - otherwise, I don't see how destroying patrols would influence the population in any way.