Other people have done their homework. There are some "synergies" that use the full skill bonus, but the vast majority of them count only the points that were actually assigned. These synergies thus do not benefit from +skills equipment.
It really is a balance issue. If +skills affected synergies, +skills equipment would be really overpowered. Or, if they took this into account when balancing it, not having +skills equipment would leave you really underpowered.
It really is a balance issue. If +skills affected synergies, +skills equipment would be really overpowered. Or, if they took this into account when balancing it, not having +skills equipment would leave you really underpowered.