grumpy, I've also found less Starports helps early game when resources are tight. Mid-game though I'm still in two minds. At that point I have no shortage of strategic resources. It's handy to be able to retrofit defensive ships without them having to leave the system, particularly for remote colonies. It's handy to have more ports to retire recovered debris field ships. I assume it reduces the need for freighters to transport goods from a colony with a base to a colony with a port for sale, so they are free to do other jobs.
Whenever you start to feel comfortable I would recommend turning the AI advisors off completely as you'll always make better decisions. The Constructors are a good example, instead of building mines all over the place, I prefer to build multiple bases in a few systems close to my colonies, as they are easier to defend, and provide shorter travel time for freighters. You'll also better prioritise builds ... why build another Caslon GMS early game if you already have plenty of stock but can see a shortage of Chromium coming in the near future. So it's great to hear you are now doing it manually. Note I never queue constructors as I find similar problems i.e. some remain idle which others still have another job to finish. I'll always select idle constructors then give them the command I want.
Be patient with base building and upgrades. Those sort of messages are intended to say the private economy is on the case, so rather than indicating a huge problem, it will just take a little time even when you are awash with resources. All we can do it help it along indirectly. So I completely ignore them and wish I could turn them off.