The 9 1/2 half inches cuts down on bee space between your frames and reduces burrcomb on the top and bottom bars. Unfortunately, it also makes your equipment unique, and should you ever grow to a point where you aren't sawing all of your own equipment out, those few initial unique boxes can become a problem in the operation.
I would wholely agree on the skipping the dovetail, just dado the joints 3/8" deep on the ends of your boxes. That will be a dado cut, 3/8" deep around the two short sides and one long side of the piece, for your two joints and your frame rest. Don't forget to adjust your length on the side pieces to compensate, you'll need to cut them 3/4" shorter than the dovetailed pieces. Nail the corners both directions, regardless of how they are milled, and liquid nail in the joints doesn't hurt at all. Liquid Nail is a little more flexible than wood glue, while wood glue does work, first time you drop a full box, wood glue joints break... Liquid Nail is a bit more flexible there.
Oh, and that is speaking from a whole bunch of years involved in commercial beekeeping. We run around 1600 hives on our end of the operation, my father is still running 1200 - 1600 hives in his antiquated age, and between our bees, what dad sends to ND, and the bees we lease out of California, we're running 5,000+ hives half the year in Central ND.
Handholds in the box can be easily sawed by setting up a jig using your dado blade, ease your piece down onto the blade, make a short pass over the blade, then lift the piece off. You can also nail cleats on the end of the boxes for handholds, but it makes your boxes a pain to stack. Be very cautious dadoing handholds on any board where you might encounter a knot. When you hit a knot with that dado blade doing that routine, things can get REALLY UGLY REALLY FAST. Still have all my fingers, but I have launched a piece or two across the room!! Oh yes... be sure and stand beside your saw during that operation, not behind the blade where it spits pieces out at however many hundreds of miles per hour.
And, don't buy budget lumber. It'll just twist and warp, and cause you problems prematurely. Spend a little more and pick up some clean 1X12 Pondersa Pine/Fir. Something that isn't going to warp and twist on you.
Initially, you should run all deep boxes, therein drawing combs for use in future broodnests. Attempting to start hives on pure foundation is not easy. They will do it, folks do it all the time, but it can be a real pain in the [beeep]. Were I you, I would run all plastic foundation; then when the mice and bugs eat it up, after your hives die, you can simply paint it with beeswax, put it back on the bees, and they'll draw it out again. If you use wax foundation, and the bugs and mice eat it up, it's gone, and you have to clean the frames up, hang new foundation, and start over. Plastic is much easier!!!
Find a local beekeeper to buy some beeswax from, you'll need 8 - 10 lbs per set of deep combs, about a pound per frame, and paint the foundation with wax before you attempt to start bees on it. Hot plate and a 2" paint brush for small operations, turkey roaster and 4" foam rollers if you're going big time!! None of it comes with any excess wax on it. There is barely enough to get them to start it, painting them fairly liberally with some good clean beeswax will make that program work a WHOLE LOT BETTER!! Don't worry if you fill the cell cups on the plastic, they'll clean it up. A little heavy actually proved better than lighter coated, they seemed to pull the cell walls thicker when we painted them heavier.
And, no the above comments about losing your hives was not intended as a wise crack directed at a newbie. We were typically spending enough on queens every year, to requeen our entire operation twice. Yeah, you do the math... 1600 hives x 2 x $15 per queen... And, everyone thinks you get rich in this business!! We're now growing around half of them.
I'd love to tell you it's rewarding and fun, but it's really a first class pain in the [beeep] anymore. We did good this winter, only lost about 30% of them from October to present. Last winter we were over 50%. And, that 30% over the winter this year was after making up losses here last spring, making up losses again when we hit the ground in ND, setting off 200 splits before end of the season, varifying everything 6 weeks before shipped, and doubling up almost 300 deadouts just before they shipped south. Had them to almost 1600 in September, dropped back to 1350 in 8 weeks before we shipped south, got down around a thousand, have set off nearly 300 splits thus far, looking at another 100+ this week.
Know several very good beekeepers that have seen far worse losses... and believe me, 95% loss on a commercial operation is not fun!
Might want to check into this class as well... Marla is fun to listen too. Pretty down to earth for a professor of bugs.
http://beelab.umn.edu/Education/Public_Courses/Beekeeping_Short_Course/index.htm