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.
Gotta disagree with you here. Adding a more or less permanent, hard pop-top (or doghouse, or whatever you want to call it) could not interfere at all with the structural integrity of the boat. It might add a small amount of weight up high, and certainly will add windage, but won't make the boat weaker (unless he is cutting holes in the companionway to make it bigger haha). Besides, plenty of people modify and strengthen their boats, and guides such as the ISAF offshore rules discuss minimum strength requirements, including the minimum number of transverse frames/bulkheads, etc. Besides, it's not like most of these production boats were built anywhere more than the bare minimum strength wise, and digging around your old boat you have a good chance to find at least a couple detatched bulkheads already...
As for the addition proposed, I am in a very similar situation. Just a few more inches headroom under that companionway hatch and I would be able to stand while cooking/changing/etc, even with the hatch closed. However I realized that by raising the companionway hatch say 6 inches, I lose ALOT of visibility from the cockpit, something very important where I sail because there are a ton of ship moorings and other blockades in the water everywhere, and it is difficult to see at night especially. One possible solution I have considered is a clear acrylic dome/bubble, which could fit over the companionway hatch. It blocks less of the view forward, and would allow me to sail the boat from inside the cabin theoretically. At least keep watch while the autopilot does the hard work in the rain.
I really like the homemade pop top idea though. It might be a little difficult to make this work, would you use pistons to lift the hatch straight up? (I've never operated a pop top myself so not too sure how this works) Does the hatch still slide forward to allow the boards to lift up? Or do you always pop it up vertically?