I wouldn't recommend it, especially since you enjoy HJKL. The problem that I have with the HHKB is that the function layer keys are in a bad spot all the way to the right of the keyboard rather than nearer to your hands' resting positions. For the same reason that Vim users enjoy HJKL you'll dislike where the HHKB puts their arrow keys.
What I would recommend instead is looking at the GH60 project in the "making stuff together" subforum. It is similar in size to the HHKB but has the corner keys which the HHKB should never have removed to begin with, they're just wasting space by not having them and leaving the corners blank (and even if someone wouldn't want those corner keys, you could always ignore them). The important difference is that the GH60 will be a programmable keyboard, so you can put the standard and function layer keys wherever you choose. This is similar to the custom ATmega controller, nicknamed the HID liberation device, that was used with Filco TKL keyboards to give them reprogrammable firmware (viewable in the "group buys" subforum). I have one of these in my Filco now and do similar to you, holding down the Caps Lock key as a FN key and then having something similar to HJKL available.
The term "Hacking" in HHKB is more for popularity/sales pitch than it actually being tailored for programming. However, admittedly only people who are more computer savvy/comfortable would be open to the idea of having to use a FN key to do such simple things as getting arrow keys. I'm not saying that you can't use it for programming, but it would likely not be advantageous in any way compared to a TKL size keyboard, particularly as it may become more difficult to do combinations as Shift+Ctrl+Fn+arrow since you now have to hold Fn in addition.
I would suggest that if you really want the small form factor than you wait for the GH60 project. Barring that, I would recommend seeing if bpiphany still has any HID liberation devices available and getting a Filco TKL to go with it. This way you have the F1-F12 keys still available on a top layer as well as arrows when doing Shift+Ctrl+arrow, but if you want to stay near the home row with Vim like arrow binding, you can reprogram the firmware to allow for that.
Of course, if you just use autohotkey, or whatever it is that you currently use to get your VIM like hotkeys, then you could probably ignore getting an HID liberation device + Filco at all and just use any TKL or 60% size (HHKB/poker size) you like.
Also, you mentioned blank keys, and I would recommend against them (and this as someone who currently has blank keys on the vast majority of his keyboards). I can touch type easily, but there are no advantages to not having letters on your keyboards except for vanity. On the other side, there are several disadvantages to not having letters on your keyboard. For example, when trying to type just a few letters with one hand (perhaps you are holding a coffee in the other), it can be difficult to find the letters that you want since you can't really place your hand in the home position to get your bearings. Additionally, pressing number or F# keys can sometimes be slightly more confusing. I use blank keys of alternating colors for every group of 4 numbers: 1-4 are in white, 5-8 are in grey, 9 to + are in white (you can see this in my profile picture), and even then sometimes I find myself sort of mentally "counting" where I should be, such as "okay... 5 is the first grey key... so I want the one next to it". This is in part because I am less confident at touch typing numbers, even though I am extremely confident at touch typing letters. It's not so bad when you just need one number or symbol, say 5 or %, but when you need to type a string of numbers, it can be painful. For reference, I type using the Colemak layout rather than Qwerty, which is why I use blank keys. However I have recently purchased custom Colemak labelled keys for some of my keyboards and for the others I mixed labelled number keys to go with blank letter keys. These provide better functionality, I guarantee you.
