I'm going to have a 80% lower engraved and after I finish milling it I'm going to have it anodized.  Will the anodizing affect the trigger and hammer pin size enough to make a difference ?

Nope. I did 2 on a nice mill with DRO following the prints (not using a jig) and had 'em both anodized. No problems.
I used an actual .376" reamer on the safety hole and 5/32" reamer on the FCG trigger pins, too.

Word of advice, I do recommend actual reamers on the holes. On the very first 80% I did, I thought "I know what I'm doing and I got a very rigid setup and sharp new drill bits" so I used regular 5/32" and 3/8" twist drill bits to save money and not buy reamers. The holes came out with poor finish and oversize to my liking. (ie: not perfect). I didn't even bother spending money on that one to anodize it. It was functional, but you could feel the play in the pind and safety when assembled. On the next two lowers I did, I used undersized bits and reamers on the holes - the holes were spot on perfect. A good lesson in don't rush and do it right... you get what you pay for.

Hard anodizing will add one half the anodizing thickness to the surface, that is if the final thickness is .001", then .0005" will be added to each side of the hole, making the final trigger pin hole size .155", and the safety pin hole .375".

If you read the drawing notes, all dimension apply BEFORE anodizing, so stick to the print dimensions and all will be fine

Anodizing will affect the hole size.
The starting and finished hole sizes and pin diameter will determine if it “makes a difference”.

Rock solid advice.
Being it could effect trigger pull and even safety, why use some drill bit of unknown quality?