Well actually, it's good. Reaper's editing is non-destructive. This makes sure that the 'undo' process is always working. If you're absolutely sure that you want to remove some files because you don't need them any more, you can use the action: Clean current project directoy, or the sws action: Project media, or by saving the project as a new file (save as...) where there are some options to copy/move the project media to the new location which also cleans up your folder.
When i'm 100% sure that i want to remove a track with it's items, i'm using this macro:
-action: prompt to continue...
-item: select all items in track
-sws/s&m: delete selected items' take and source files (no undo)
-track: remove track
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