Yeah...definitely design your system with a sump. They're awesome to have. First, it gives you more water volume. Second, you can incorporate a refugium to absorb excess nutrients and breed free food. Lastly, you can hide all of your equipment under the tank, in the sump.
I designed mine with a sump and have seen pics of sumpless 40's and I'm very glad I chose to go the sump route. If you're planning on building your stand, definitely make it on the taller side so you can fit even more stuff in there. I have my skimmer, a reactore for carbon and gfo and a DIY kalk chamber plumbed into my ro line under there. I also have my three pumps in it (return, skimmer, reactor), my skimmer and my heater.
I also have a two stage refugium in there. Basically, I built a pvc stand for a 5.5 gallon tank that sits in the sump, straddling tow of the sump sections (one half of the stand is in the "return" section, the other in the "live rock" section). It sticks out of the top of the 29 gallon by quite a bit with only the bottom inch or so of the 5.5g below the rim of the 29. I have my return t'd off to feed the 5.5g which then flows through a pipe in the refugium (yep, the 5.5g is drilled on the bottom) down into the live rock chamber which is directly beneath it in the 29.
It'd be a lot easier to see what I'm talking about if I posted pics. Anyway, the point being, you can do a lot with a sump. I would also drill the main tank instead of relying on a siphon for drainage. Just seems a lot safer with regards to spills/overflows IMO. I'd worry about what would happen if your siphon breaks for some reason; basically, you'd be looking at your main tank overflowing until the return pump pumps all of the sump water out. Opinions will differ on this matter, though.