Did you overset the neck? If the set is right, then you need to shim, unless the top is collapsing into the sound hole. In that case some internal repair would be needed.
If it has too much fall away, you should do whatever it takes to make it right. Your investment in time so far has nothing to do with your obligation to your client. You held yourself out as being able to do the job right; you gave a price; you have an obligation. Stop looking at the clock; some jobs just go that way. Your charge should include that possibility. Look at the long run of neck resets and charge for the long run.
If the neck reset is perfect, I wouldn't be that concerned with shimming the extension unless the customer plays up there or doesn't like the fall off.
If a shim needs to be added, I don't totally eliminate the fall off as a thick shim doesn't look that good. If the guitar has fretboard binding it is hard to not make it show.
If a shim is required it is best to install on the extension when the neck is off. Of the resets I have done I'd say only 10% or less actually needed shimming.