Electronic – Should Shielding GND be isolated from circuit GND

Divide your board into those discrete sections: PLL, Analog, Digital, and IO. Try to keep all of the copper (signal & power) for each section separate except where they require interconnect. Join the power to each sub-circuit only at near the power supply, within the sub-circuit and at chip when possible. Bypass each at the chip grounds with a cap or two (you might leave an extra footprint here for test).

You may find that the layout doesn't permit total separation of sub-circuits. If so, at least try to use a wider trace to supply the split and filter where necessary.

If you would connect the two grounds it's not really useful to have an isolated converter in the first place. It would be like two supply voltages on the same circuit, like +5 V for the logic, and +12 V for relays, or something like that. The two power supplies may also only share their grounds, but that way they're not isolated, not even if they would be otherwise floating, like batteries.

Isolation is often for safety reasons, or to avoid ground loops, like Tony says. One reason for using an isolated converter may be to have a floating output so that you can reference it any way you want. If it's a 5 V/ 5V converter for instance, then connecting Vout to the input's ground will give you a -5 V at the output's ground.

So if you had a good reason to have isolation, don't connect the grounds.