In most cases, it isn't going to be critical, because low frequencies are not directional, so it is doubtful if you could tell the difference by sound alone, assuming that it is set up properly and functioning correctly.
However, over time, gravity is likely to cause the woofer to sag, and with it down firing, it is likely to become off center at rest, and then it will not be able to perform as well as when new.
Also, with it down firing, you will need some way of raising the woofer off the floor, so the cabinet is likely to be more trouble to make.
For these reasons, I would probably go with a front firing woofer, if I were making it myself, unless there was some particular design issue that I needed to accommodate (e.g., if the cabinet were cylindrical, then I would put the woofer at the end of they cylinder, etc.). In my case, however, I happen to currently own down firing subwoofers (SVS CS-Ultra). But that was selecting what was available, not making it for myself.