I keep having a problem with this. It just doesn't make sense to me to have the same exact penalties for resources as credits with regards to fleet logistics.
The fact that you can spam trade ports, while the effects of refineries is capped means that you can mitigate the effects of logistics as far as credits. You can't do that with resources. Thematically (sp), an empire that is maxed out should be at the peak of the mountain. You should be able to put more into R&D. As it stands now, the most efficent time normally as far as that goes is about half way. This seems a bit backwards.
Also, it makes sense to tax the money. Just look at the cost of any war..which if history is any guide, is when the military is at its strongest. It costs far more materials to build a ship then to maintain it. Metal and Crystal are raw materials.
As far as gameplay goes, it slows down the end game quite bit, and unless you are in a constant state of expansiion (and even then), it makes it very hard to do research.
There should be a penalty, but the fact that credits and materials are obtained at a far different rate, it doesn't make sense to penalize them the same way.
Just my 2 cents.