Just wondering if anyone has any reasons why I shouldnt do this...
Playing devil's advocate: because the deck and cabintop are important structural elements in the overall strength of the boat as designed. Assume nothing is superfluous and respect the designer of your boat; leave it as designed. It is one thing to replace or repair a defect, it is another thing to alter the basic design of the boat.
If your boat does not suit your purposes, sell it and buy another boat designed to have a doghouse/raised cabintop. The transaction costs are not that great.