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(Thunderhammers, vibrocannons, Haywire, emp etc) I would guess no as ap- is still a stated AP but have you seen it played otherwise.
Sorry if this is settled in an FAQ or indeed the rulebook...
I don't think it is that obvious a question but Thanks for any help regardless.

Close combat attacks don't have an AP value. So no modifiers either way.

I am not sure i fully understand your question here, but as far as Haywire goes, its clearly stated that you only roll to hit. The next roll is a replacement for traditional armour Penetration, skipping the mathmatics and glancing vehicles on a 2+, Penetrating on a 6+.

AP - is not the same as "No AP value"