I just got one of the black pearls, looks like it does increase weapon attack by 1%. However, I do not know if it scales to the BASE attack of the weapon or the TOTAL attack of the weapon (base and the upgrade bonuses). I did not take note of my attack beforehand so I am not sure on this.
As for the gem stacking, my guildy said he can stack 2 gems on the same piece of equipment but I am still working on confirming that.
EDIT: just confirmed that the gems only scale to the BASE attack of the weapon.
Example: so let's say your bow is 600+1300(made up these numbers, easy to work with). Now let's say you put a 1% black pearl (increase attack of weapon by 1%) to the weapon, your bonus would be 600*0.01=6 attack.
So still, the bottom line is, these sockets are small bonuses, and will not transform you into a god by any means.