Do design change I presume. The 109K manual from Oct 1944 already notes the doors for both the u/c and t/w, but it's not seen on the photos available for early a/c, inc. the 330 xxx block in which the first machines were used for testing in good concrete airfields in the summer of 1944 (109K entered production in August). And mind you, already the 109G was designed for wheel well doors, there are few examples with them. Note the 109G has a straight outside panel on the wheel well vs. the 109F which has a all-circular one. Clearance was not an issue, since they were far from the centerline rack..
I suspect either the doors were not available in numbers in the early production, or there was not enough replacement parts in stores for the units when the plane was introduced, so if something went wrong with them, the crew would disable them. When there were enough supplies later on, I think it was no problem to retro-fit the doors on older planes. From the 332 xxx series onwards, I can see them appear quite regularly though.
