First of all, if you were checking a connection based on head pull-through strength, you would take the WH (design value) from Table 12.2F as you mentioned, and then you would calculate the adjusted pull-through strength, WH', based on the factors in Table 11.3.1.
For ASD: WH' = WH x CD x CM x Ct
and for LRFD: WH' = WH x CM x Ct x 3.32 x 0.65 x lambda
At this point, WH' is already accounting for a safety factor, and you would compare this value directly to your factored load from the load combination that you're checking.
Now to try to answer the safety factor question:
I could be wrong, be I think, if you were to calculate the LRFD value, excluding the strength reduction factor, phi, which is 0.65 in the above equation, that would essentially give you the nominal capacity for LRFD design. If then you multiplied that value by the ratio of your factored load per ASD load combination to the associated LRFD load combination, and then further multiplied by the ratio of CD/lambda, I think that would give you something of a safety factor per ASD. If the ratio of your factored load per ASD combo to LRFD is 0.67 and the ratio of CD/lambda is 1.25, then that makes the safety factor 3.32*0.67*1.25 = 2.78. Again, I'm not sure this is exactly right, but it seems logical to me.
Again, for this particular calculation, the safety factor is already accounted for. This is the case for most strength calculations per the NDS code. One exception, though, is wood shear wall design where you take a nominal unit shear capacity and then either divide by a reduction (safety) factor for ASD or multiply by a resistance factor for LRFD. In that particular case, the "safety factor" is 2.0.
And yes, this stuff is all confusing, especially when you're used to steel design, for example, where the safety factor (omega) is explicitly defined. I've caught other engineers not applying the reduction factor for shear wall design. They assumed it was already accounted for like most of the NDS code.