Are there any disadvantages using magnetic couplers instead of opto-couplers?
The magnetic ones (and some other non-optical types) transfer only changes to the state. Although that page you linked says that they work to DC, that's only because there is a latch on the other side that maintains the last known state. Consider the NVE IL710



In some cases, this could be a deal killer. 

Secondly, another disadvantage is cost. You'll never see a magnetic type in a cheap SMPS controller because they're more expensive, even if the other quirk didn't exist. 

Thirdly, if you're designing things that need to live near high currents or other things that cause large magnetic fields (not uncommon in applications that require isolation), you'd better check out the magnetic field immunity: