I've disabled a number of packages, but kept seeing their items - it was a while until I realized they were history items. Maybe the catalog doesn't keep track of the parents of history items, but it's a bit confusing to see results for sources you had disabled. Especially since you can only effectively remove them by clearing the history, which may be painful for a user with lots of usage and useful history.
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This is expected behavior. For some reason, you may want to re-enable item's parent package or just disable it on a given machine, but not on another one. This is in case KP is installed on a USB device for example (since it allows user/machine-specific configuration).
Use Ctrl+Del to delete a single item from history, as described here.
In a future release, the Catalog will filter out items that are in the history and orphan. Which means such an item will remain stored in history but that it won't be visible in search results unless its parent package is loaded (i.e. existent and enabled).