let say troll without armor , only it own 1 natural armor , is shot by mossberg shot-gun ( ap +5 )

for sake of damage resistance - its armor is 6 or 1 ?

It's not like the guy has separate armor scores for armor, natural armor, deflection and what have you. It's just the armor score.
So yeah, he has 1/1 armor, and being shot with something with AP +5, it becomes 6, quite obviously.

I agree. In the same spirit, if the troll gets shot with a weapon that has -1 AP, he loses his only point of natural armor.

Armor is armor is armor is armor. Doesn't matter what the source is, if the troll has 1/1 armor, then the troll has 1/1 armor, and it is indistinguishable from any other 1/1 armor (Excepting hardened armor of course)

Eg. don't shoot a troll with flechetts.

Remember, flechettes are intended for civilians. Trolls aren't really quite that. (*duck*)

s/civilians/unarmored targets/

Critters.