I work in the building industry (several decades now) and I would have required a removal and replacement with Felt or some type of high performance underlayment. Underlayment (felt, ice & water shield, Titanium etc) is an integral part of your roof system and can help eliminate/reduce water penetration for the life of the shingles. It's such a CHEAP and EASY item to apply (before the shingle of course) I can't imagine a company taking that kind of shortcut. If they skimp on underlayment I would question everything they do.
It's important to note in some areas roof underlayment is a required/coded portion of shingle to sheathing installation (not required when applying shingles over shingles but still suggested) and building inspectors can demand a removal and installation if it comes to light. You may have saved $1,300 today but at what cost for the future? Keep in mind that water penetration can be a slow to show problem and rot, mold, mildew can be a HUGE (and expensive) problem later down the road.
Also note that some shingle manufacturers require the underlayment to be installed for the warranty of their shingle. All it takes is one slight installation mistake and you have no warranty down the road should there be a shingle failure and this is regardless to the actual REASON for the failure. The shingle manufacturer would LOVE to not pay a claim due to "improper installation" by the roofing contractor.