Unless you keep the arched roof supports, you will weaken the overall design, not strengthen it. Why? Because the strength lies in the uninterrupted arch of ribs over the ceiling of the bus. Take out a couple of them for entry into a "second floor" created by the van top and you'll be okay. But cutting them all out will not help the strength.
That being said...
Unless you plan on entering a demolition derby with your bus, it shouldn't make much difference to livability
. The biggest disadvantage you'd have is no extra cabinet space along the sides. You'd still be reduced to using the original height of the bus and have to fit the cabinets to the remaining curve. You'll have loads more head room, but that's just wasted space in the center aisle.
The type of raise Smitty, Millicent, and others have done gains wall space as well as ceiling space. This is very important in long term living.
If you want to add a van on top, then go for it! It's YOUR bus. If it makes you happy, then it's a great decision. Just weigh the pros & cons of how you plan to use the bus (party bus, tailgater, camper, mobile home, etc.) before you start cutting.