It doesn't deal damage directly to HP, it deals damage equal to 5% of their max HP. So if your B2 is applying buff immunity then Nute's zeta will add some bonus damage on top.
Example: B2 uses Mow Down and lands buff immunity on a Kenobi with 40k HP. B2 does his normal damage plus 2k bonus damage from Nute's zeta.
It is one of those Zetas that doesn't feel like it is doing much, but then you look at their team and realize that B2's constant AoE's have actually stripped all enemy's protection and set GG up for easy kills.
Nute works pretty well with GG. Here's a clip I recorded a while ago of GG taking on JKR full auto. This is with G13 GG against a full G12 JKR team though, so can't say it is zNute making the difference (it's definitely GG). Just to show that he's a pretty good 5th if you want to save Droideka for somewhere else (like RJT in GA):
https://youtu.be/voNMo6ZYw0c