They didn't get rid of it. It was never introduced.

At the time there were many types of firearms. Only the heavier version used a fork rest. If I'm not mistaken (I'm not an expert on European warfare) the heavier version were mainly used on land against heavy armour. There were lighter versions popular on both land and sea (and in fact more common on land as well). These did not need a fork rest.

Japanese lords also imported lots of guns from Southeast Asia. Looking at the designs of Southeast Asian firearms, they very probably influenced Japanese designs and possibly the European guns manufactured in the Asian colonies. They also did not use fork rest.

The English terms for lighter guns that did not need a fork rest was caliver, which is the term William Adams used to describe Japanese firearms. If the terminology is fairly consistent, then we can actually see that even in Europe, firearms without a fork rest greatly outnumbered those with a fork rest.