You only reason they would need your HST number is if you were selling them something that you charged HST on.
Unless - does the software print out or email receipts for customers? If so, this is probably to include the HST number on the transaction receipt which in of itself can be helpful to customers who claim ITCs.
You have to include your HST number on any receipts, invoices or contracts with more than $30 of taxable goods. If you attach the slip to an invoice that has the HST number you're fine, but if the slip is the only thing you give to your customers and you charge more than $30 it *has* to have an HST number on it.
I always attach slips to invoices with an HST number on it, so it's a non-issue for me.