To disable a channel from notification:

Step 1: Log in to JIRA Server as an administrator

Step 2: Choose Settings button at top right corner

Step 3: At drop down menu, select System

Step 4: At the left hand side, scroll down until Slack Integration option > choose App setting

Step 5: Choose Access control tab

Step 6: Enter channels list in to text field that you don't want to setup notification in project setting (start with # for public channel, ? for private channel). Then click on Save button