Well, your ped really should be checking your DD's girly bits.
When both DS & DD were infants, the nurse would instruct us to take their diaper off for their weight check, on again while waiting for the doc to join us in the exam room, and then off again for a few moments during the exam.
The ped (we've always seen female peds) usually requests the dipe be off to check their hip rotation, quick glance at the labia, a gentle tummy exam (sometimes the dipe can be on for that one), and any concerns you may have about that area (like yeast). Then the dipe goes back on. It is never invasive, but it is a normal part of the well infant exam.
We saw 3 different docs in the first practice we went to, and another at our new practice, and they ALL do a quick check of the diaper area, regardless of the child's gender.
I can understand missing it once, or even twice, but if your DD has been through multiple exams and the ped has NEVER checked her girly bits, then I'm pretty sure they aren't doing a complete exam.