I think your problem may be with the type of CD/DVD's you will be using.
Originals that you buy and come with all the bumph in a box are actually pressed like an old time vinyl then a coat of lacquer is put over the playing face. These should not delaminate as you drill thru them.
Ones you buy in bulk packs to burn yourself are made by sandwiching a layer of very thin foil between two plastic(?) discs. These very easily delaminate. In fact you can easily get the two bits of plastic apart by prising around the edge of the disc with a sharp instrument.
It is the porous nature of the lacquer that was used and the bad sealing around the edges of others that make discs not as long lived as they should have been, on a bad disc you can usually see an oxide coating forming on the metal substrate, the start of the delamination process.
So in theory, your home made flywheel could easily fall apart in the not too distant future, purely because of the laminated make up of the discs, unless of course you are going to bolt them together.
John
