It sounds genuine to me.
When you take work in at a bike shop, you give it your best guess, because you cannot DO the job before you Do the job.
It is also in the nature of things that quite often the person on the desk who takes your work in, knows less than the person who will do the job, and therefore your initial point of contact doesn’t know what the common stumbling blocks might be, and therefore isn’t able to pre brief the customer of possible issues. Then again the most brilliant bike mechanics can be less than communicative……And, with the best will in the world, when you come to do any job, problems that you could not see before sometimes become evident, and you have to change the game plan.
If it is alloy nipples involved, and especially the fangled Mavic ones, then I think you’d be very optimistic if you were trying to use them twice. Stainless steel spokes and brass nipples are usually no problem, but best practice would be to go for new every time.
I would guess they mean the nipples are furred up with alu dust and not reusable. I doubt they are trying to have you over.