But I'd expect a big part of the nets are not connected to the ground? I mean in my hobby designs a majority of them is, but let's say if you generously use decoupling capacitors, then that might not be the case?
Typically, you need dedicated circuitry (and usually inductive coupling) to provide full isolation, but if the circuit is using this layout then you can still choose to ground the normally-isolated side for probing.
A truly "floating" circuit would be something battery powered, or galvanically isolated from mains Earth (e.g. by an isolation transformer).