Is the commission that an accountant takes for nominating and selling an accounting program permissible or impermissible, whether the buyers know about it or not?

If you do not receive a salary from company owners for nominating programs, and if that is not part of your work for them, then there is no harm in taking a commission if the sale is made through you. You must, however, strive to offer sincere advice and choose the best and most beneficial programs, for "the consultant is entrusted," as stated in the prophetic Hadith.