To make sure that web store pages load as quickly as possible, it is best a practice not to put more than 50 items in each category. Set up enough categories and subcategories to make browsing easy for your customers. The Web store displays up to 1,000 items per category. Users are permitted to add more items to a single category, but any items over the 1,000 item limit only display in search results. This information is also available in SuiteAnswer ID:27769
Too many items in a category sometimes causes performance or slowness and some difficulty opening/editing the category.
Here are some options how to remove item in category in Site Builder.
1. Navigate to List > Website > Categories > Edit
2. Click on the item > Click on Remove button
1. Navigate to List > Website > Categories > View or Open the Category
2. Open each item record assigned on the category and remove the category on the item record
1. Do a CSV import to update all items associated to the category. Please see SuiteAnswers ID 42718, same steps are applicable on how set to the site category value to blank. Just replace Item Drilldown Template to Site Category.