As folks have said, the CRs of creatures are set with the assumption that PCs are equipped close to the values given. As folks have also said, as long as you make adjustments to the challenges, you'll be okay.
One interesting thing is that DMs can run into the same "underequipped" problem even when PCs have items of a monetary value equal to or even greater that given in the DMG, if the items they have are expensive.
For example, if a PC is supposed to have 19,000 gp worth of gear, there's a huge difference between "1,000 gp worth of miscellaneous equipment and a +3 ring of protection" and "1,000 gp worth of miscellaneous gear, three 2,000 gp items, and three 4,000 gp items," even though the monetary value is the same. (I tend to prefer few-but-powerful magic items for my players, but, as I said, it plays the same as if they're underequipped.)
Another thing to keep in mind is that being underequipped has a disparate impact depending upon class. An underequipped fighter will have a much harder time meeting challenges of his CR (or close to it) than will an underequipped rogue. (Clerics and arcanists fall somewhere in the middle, IMO.)