It all depends on the amount of product turnover your store of choice has, for example. My local Wal-Mart still has New 3DS units from launch day so those will be running 9.0.
There's a thread for checking the serial number to pinpoint what firmware the N3DS is running.
There is a HUGE possibility of getting a N3DS with 9.0 Firmware in either black or red!!! I literally just bought one last weekend. A lot of Walmarts have PLENTY. The one i went to had over 15 Black and 20+ Red. And half of them were 9.0 firmware. I just explained to the worker that i wanted to look at the serials to see if one matched what i was looking for (insert reason). My reason was older serials allow you to run homebrew. Not that she knew what i was talking about lol.
If you are looking for <9.2 in stores then you are probably out of luck.
You can try ask at online stores for the serial. They are shipping still higher versions.
Many will get 9.4/9.5 in stores. It might depend if you are in usa/europe.
it all comes down to how popular your area is with nintendo fans. I remember release day I bought mine and I managed to pick up a 9.4 system (hence the firmware list, luckily I was able to return it ). My point is that it's worth checking stores in your area before assuming they won't have one.
Also, a $50 markup on a $200 item? Yeah, good luck with that, especially when it's been established that 9.0 N3DSXL systems are not rare. Hell, even with 4.5, you'd think that'd be somewhat rare in 2015, but nope, depending on where you live, it's perfectly possible that you could still get your hands on a 4.5 brand new unit without too much fuss. People seem to think the 3DS sells far better than it does when sales have actually slowed down considerably in the past couple of years.