The pedal will function 100% normal with just the 1 leg desoldered. I say desolder the 1 leg incase you dislike it and want to put it back in. It's easier to re-solder 1 leg than 2.
However, if you like it, I'd recommend desoldering it completely, or cutting it out. Your choice.
As far as bass loss, there are a few things you do. I only did a very minor bass mod to mine. I plan on changing a few things around. Because I increased the 4.7k resistor to 1.5k for more gain, it tends to thin it out (and that's why Keeley uses a huge .22uF cap in C6). For increasing bass, try .1uF caps in C2, C3, and C8. Also, these might help you out:
http://www.robertkeeley.com/audio6l6/sd1mods.html
http://www.geocities.com/overdrivespider/SD1/sd1.htm
If you do the gain mods on R6 (changing the 4.7k resistor), you'll at least want to change R2 for something like 620k or higher. There will be more noise and it'll start to "leak" even when the pedal is off.
The biggest difference, IMO, is changing the diodes. That's where you'll get the most drastic difference. LEDs are loud and powerful. Germaniums are quieter and softer.