Can you get a HHKB in a physical store in Tokyo

[In Stereo!]

If yes, where? Would there be some choice to that or is this more of a rarity and should be happy with anything resembling the HHKB?

[hcry4]

I assume you can find it somewhere in Akihabara.

[nar]

Here's the official list of authorized HHKB dealers in Japan
http://www.pfu.fujitsu.com/hhkeyboard/showroom.html

So from that list, all the stores are in Tokyo, there's Cleverly in Akihabara, I believe there is actually a guide in the wikis on how to get there. There's also AssistOn in Harajuku

Here is also the list of Realforce dealers. They might also have stocked some HHKBs as well
http://www.topre.co.jp/products/comp/key_shop.html