How fortunate for you my friend that i had a similar conundrum and already did all the legwork for you.
You can definitely register a DSi and a 3DS to your Nintendo account.
If you have both a DSi and 3DS connected to the internet at the same time, the best solution is to convert your stars into Nintendo points vouchers, buy games on DSi ware, then licence transfer those to your 3DS, at which point you can delete and redownload them on your 3DS as many times as you want.
If you want to see my research, I drew up a handy dandy google spreadsheet of DSiWare games I'm interested in (organised by name, point cost and review score), 3DS star points rewards I'm interested in, and my current top picks of what I'm considering buying.
The colour key is:
Green = I bought it
Grey = No longer available on EU Dsiware shop, for whatever reason
Red = Decided not to buy (3rd sheet only)
It seems to me that if you have an amount of both points and stars, the best solution is to convert your stars into points (the ratio is that 4 stars buys you 1 point), then buy the DSiware games you want, and licence transfer them over. The ONLY exception to this value ratio is if you specifically want Aura Aura Climber, that's the only game on both DSiWare and Stars Catalog that's cheaper to buy in stars.
THE one major annoyance I've discovered is that there's a limited amount of space on the 3DS internal memory for DSiware games. I doesn't matter if you have a SD card with infinite gigabits, you can't play DSiWare games off the SD card, and the internal memory allotment is annoyingly fixed.
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Topic: What to do with my DSi points
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