Yes, Boober may be a self-proclaimed coward, but when the time comes he's a mensch. He's even more afraid of what will happen if he hides under a rock than of going out and facing Silly Creatures. Plus, he has children now (he regards Poncle as his child too; Fraggles consider upbringing more important than genetics) and he'll do everything in his power to protect them. As in Marooned, Boober can be brave for someone else.
Also, he just might have thought that Gobo would stand up to the Silly Creatures, which would be less likely to gain their sympathy than looking piteous and throwing themselves on their mercy.
I think that Fraggle water has a bit more character than filtered tap water, since it's heavy with minerals and who knows what else. Unfortunately, lately there's more who-knows-what than they like.
And...well, who says the Fraggles could possibly make themselves visible to those Silly Creatures? Doc only saw Gobo after they had touched each other, and that happened on an emotional level before they touched physically. The Silly Creatures Boober tried to talk to were not open to the idea of furry little troglodytes living in the ground they have mineral rights to, so they were simply unable to see Boober. What would it take to change that attitude, and do they have the time to try?