Yes, but depends on file type.
If you change the metadata of an image (in the image or its sidecar) externally from Lr then presumably you are storing the new metadata in that file or sidecar. But Lr doesn't know about that new data. Lr stores metadata in its own database. Lr should notice the data has changed externally, and show a little icon in the grid cell. Then you'd have the option of either overwriting Lr's stored metadata by accepting the changed metadata from the file or the sidecar, or the reverse, overwriting the metadata in the file or sidecar.
Since you changed it in exiftool you'd probably want it, so you'd overwrite. If the icon doesn't show up right away, you can use "read metadata from file" to get that info into Lr.
Once Lr has the metadata in it's database then yes, you could delete the sidecar.
But note that some files don't typically have sidecars, like JPEGs or DNGs, and the metadata is stored within the image files themselves. I can't recall if exiftool can write sidecars for these file types (I think it can), but Lr might not recognize them.
There is at least one plugin (Capture Time to Exif) that lets you use exiftool from within the plugin right in Lr, BTW.