Repair costs in X3 are ridiculous, you have to pay the percentage of the purchase cost you want to repair (i.e. repairing 70% damage costs 70% of the cost of buying a brand new ship). I got fed up with it and wrote a script allowing me to repair at a cost of 10 Credits per hull point, which is both notably cheaper, and (to me at least) more logical. To use, go to your ship's 'Special' commands, where you will find an option to "Repair by Hull Points".  If you are docked at a shipyard you can then repair your ship at a rate of 10 Credits per hull point lost.