I personally haven't heard or seen anyone that has hydrographic dipped the side panels of their MPC 1000, but that doesn't mean it can't be done as I seen plastic wheel tirms, air intake covers etc that have been hydrographic. You best bet would be to speak a company that specialises in hydropgraphic dipping to see whether it is possible, but I'm pretty sure it should be possible to hydrographic the plastic side panels.
Also you might be worth looking at buying a cheap pair of second hand side panels for testing, just encase it doesn't workout right and ruins your original side panels.
MPC 1000|128MB Ram, 100GB HDD, JJOS 2XL
MPC 2500|128MB Ram, 40GB HDD, CD Drive, JJOS-XL
MPC 2000| 32MB Ram, Version 2 LCD, 8-outputs & EB16 FX Expansion