It would require some re-balancing on starbase numbers and piracy/trade defense, but I would unironically support a universal collection system, where all resources must maintain trade links to the empire core to be collected.
Main exception would be non-tangible communication-resources, like science (or unity).
Pirates non tangible! They create themselves out of nothing! I do disagree though, you should be able to interrupt the pooling of research and unity as not only is physical trade is interrupted but you are in effect cut off from those systems while pirates are present so coordination between colonies falls off.
Seriously though, the issue with piracy is how it scales and that it only affects trade which in turn means on certain empire types encounter the issue. Logically pirates, if they could even exist, would affect every empire where colonies are not self sufficient and where resources have to be moved to support development, an example is alloys are produced at more than one colony but the ship yards are in another system.
The simplest fix in my book is to eliminate pirates from spawning in occupied systems. This would make them an early game threat and they could exist for all empire types. In effect they encourage the claiming of adjacent systems and bringing order to space. However we need to preserve the espionage method of inserting raiders into another empire's space. Think of it like Civilization barbarians, eventually there just in no place for them to live and develop.
Currently for my empire designs that do have trade I use trade routes to train admirals and sometimes use multiple overlapping small fleets to keep multiple admirals training when war fleets are parked. Explanation, if piracy requires me to use a dozen ships on a route I will instead split that into two or more fleets so that multiple admirals can train simultaneously.
