This is possible, and supported, however it will be tricky if you wish to UPDATE the lookups post deploy via the deployment server.
There is a deployment server option to exclude folders/files from updates:
excludeFromUpdate = $app_root$/lookups
This will populate the lookups directory if it doesn't exist, but if the app already has a lookups folder it will completely ignore it. If you have a single lookup file that you wish to exclude from the deployment server, you should be able to specify that particular lookup:
excludeFromUpdate = $app_root$/lookups/mylookup.csv