It uses more juice for a few reasons:
Code needs to travel further:
The machine is booting from Slot 1, so it's running from Slot 1, but all the data is stored on Slot 2, so the machine is doing more work than reading from Slot 1 by itself.
SD cards require power:
And so does the flash cart, the battery in the flash cart (if applicable), and the Passkey. But the biggest draw is that a 1gig microSD card requires considerably more power than a normal DS cart.
I've noticed a pretty substantial difference in play time, I think, since getting my combo. This might be because I'm using the device more and it just feels like I'm running it down faster, but I do think that there are fewer hours between chargings of actual play times. I haven't actually timed it. I think someone else has though, search a bit and you might find a post about it already.
To conserve power, set the brightness to the lowest setting you can stand. I always set mine on brightness 2 (out of 4) anyway. Follow some standard LiOn battery power consumption tactics: don't let it discharge completely, etc. Search google for other things. There's nothing else much you can do. Hopefully the new Slot 1 devices will do better in terms of power since there's no flash cart involved and the code is coming straight from Slot 1. The only extra battery use is to power the micro SD card, so hopefully these will need less juice.
