No, it's not a functional problem,........It just looks bad. I tried to fix it in about 2006 with an ECO (Engineering Change order), but its common on guns in the last 25 years, there are a lot out in the world like that. I'm not sure the change was ever acted on, as I was transferred off the 39 product line, almost as soon as I started to support it.
If I recall, the hammer hole is a few thousandths larger than it needs to be. That happened with a change in vendor for the screw. and the c'bore depth for the screw head was not dimensionally correct for some time too.
You can remove the screw mounted hammer, and make up some shims out of brass or plastic shim stock to cure the problem. I had to do just that for my early 80,s era 39M. It's not hard to do, just takes a little time with a punch set or sissors.