Does this adversly effect accuracy?

Swiss
If I am understanding your question accurately the answer is no.
One example I may use is the .284 Win cartridge, verys short neck and made to fit in a short action so much more of the bullet is seated than lets say a .280 Rem or a 7mm mag.
I am loading for the .284 with a lot of success and all of my loads are seated so that the boat tail and a good portion of the "bearing" surface of the bullet is below the neck, accuracy is great some 3 shot groups in the .575" range.
Another example is my 375 H&H, magazine length dictates that I seat the bullets deep to function through the magazine, these are also shooting .5" and .75" 3 shot groups at 100 yards.
Hope this is what you were asking about.

Assuming that you mean the base of the bullet extending below the neck into the shoulder area (or sometimes even below the juncture of the shoulder and body), the answer is that it is more often the case than not, and has no particular bearing on accuracy.

This of course varies with the particular caliber and cartridge. It is virtually impossible to seat a "normal" .224 bullet below the neck/shoulder juncture of a .222 Remington due to its relatively long neck and the realatively short nature of .22 bullets. On the other hand, it is virtually impossible to seat a typical .30 caliber bullet to an acceptable overall length in a .300 Winchester Magnum without it protruding below the neck due to its relatively short neck and the longish nature of the bullets typically used in it.

Only time I can think of that seating below the neck is a problem is with cast bullets with slip-on gaschecks. If the gascheck comes off inside the case the bullet is probably going to lead and the gascheck can actually end up partially plugging the bore - which is a real problem for the next shot fired.

I've shot thousands of gas checked bullets seated below the neck without incident. The gas check rarely comes off inside the barrel because gas pressure is pushing the check against the bullet.

Benchrest shooters don't like to seat below the neck because the wall thickness at the neck/shoulder junction tends to be thicker than the rest of the neck (they refer to this as the dreaded donut) and difficult to control. This can lead to inconsistent neck tension in a turned neck chamber. However, most hunting rifles have generous clearances in the chamber neck, so it is not an issue for hunting rifles.

Every 6.5 bullet I shoot from my .260ai is seated below the neck. So far accuracy has been exceptional, most groups going under 1/2moa.