It should. You'd definitely have to enable the ir feature, and likely not have full functionality. The color buttons likely do not work, as I don't believe there is firmware for them to work.
The color buttons work fine, IIRC all the buttons work fine in IR mode. You can't pair it or have the Hopper program the TV or AUX codes but you can program them the old fashioned way.
Other than being IR only, 20.x and 21.in IR mode) have EXACTLY the same functionality of the 40.0 for controlling the HWS. Just make sure they are set for address 1.
In my living room, I recently dusted off a 21.0 when a 40.0 stopped working. I have always used a 20.0 for the basement HWS(clear line of site). The day it was installed, I paired the 40.0 that came with the basement HWS as an extra remote for the bedroom joey (hidden behind the TV - no line of site).
As JSheridan noted, the HWS cannot program the 2x.x remotes, you have to resort to looking up the codes for your TV/DVD/AUX in the manual and keying them manually.
I have been using my 5.3 IR W/ my HWS since I got it (HWS). It is line of site, and doesn't have the colored buttons, but has performed yoeman duty whilst I use my 40 RF in the master bedroom.