I noticed something similar myself post FC update, but was told I was misremembering, so I assumed that I was. Good news if it's the same thing you're seeing: They're not gone, they just don't show up on your Nav immediately, which is how I remembered it working (provided you'd properly scanned the system/planets first, of course).
Approach the planet in SC until the little "target circles" show up on the surface, then move your ship's nose around until the one you're looking for "pops" and lock on to it. It can be a bit of a bear though if there are 40 geo/bio sites on the planet as well.