[Alneyan]

Another possibility to explain your economic shortages: have you lowered your resource gathering characteristics and/or your maintenance aptitude? Doing so would cripple your economy, especially in the case of maintenance, since lowering maintenance will kill your economy very quickly.

Along the same lines, what is the current happiness levels of your worlds? Happiness is paramount to determining resource income, and so the number of ships you can safely supporter. Or have you taken something besides "peaceful" as an happiness type?

Besides such odd Empire setups, I see no other reason why your economy would be in such a poor state, if you have expanded well and developped your colonies.