Well Hathcock preferred the 30.06 Winchester M70, not the 308 Remington M40, and as with anything you will have exceptions to the rule.
Realistically on the whole bolt guns are accurate than the semi autos regardless of the era. One thing that modern shooters generally fail to consider is that there have been huge advancements in ammunition accuracy since the 60's. So its fairly useless to compare vintage snipers with modern match ammo or worse yet hand-loads. I have a "repro" M40 that is very accurate .5-.75 MOA with hand loads. However, 60's era M118 match didn't use modern 175 SMK bullets, temperature insensitive powders etc. so that doesn't really give me an accurate idea of what a VN era sniper would be shooting. From reports I have read the original M40 was typically a 1 moa (ish) gun when it was issued with the 60's era m118 which is comparable to other 70's era bolt action sniper systems from other countries.
With regards to the zero, doctrinally speaking the marines at the time used a 500 meter zero with the M40, and held over for 600 meters and held under for ranges shorter than that, the TM has a nifty chart for holds on a standing and kneeling target. Then again, the average sniper engagement range in Vietnam IIRC was something like 300 or 400yds on average (yes yes there were many "long range" shots too, but they were the exception not the rule) and I'm sure some of the better shooters did zero at 600 meters or even longer as the situation dictated. Basically take anything that Hathcock said and put it in the context of he was the best marine sniper in VN, not some average Joe sniper.
The main deficiencies of the original M40's were issues with bedding like the M21, durability issues with the redfield accurange scopes and the fact the scopes couldn't really be repeatedly adjusted for elevation or windage in the field. Again, all of those issues were rectified in the M40a1 which IMO was the first "modern" US sniper rifle.
Then there are the whole host of training issues with US snipers in Vietnam but thats getting off topic.