Depending on the type of socket there's some buffering latency. Nothing to worry about for most applications. The nice advantage is that with IP socks you can have the GUI on a completely different machine from your DSP
Afaik some disadvantages/issues worth mentioning:
There's no equivalent to a "bang" in most toolkits, but a push-button does the job okay if you act on the button_down event.
Some of Pds GUI objects have "hidden" built in capabilities, like VU is more than just a bar graph display, it does some of the slugging necessary for a proper VU response. You might need to add a bit of extra code to some of your GUI display objects like that.
Pd slider GUIs don't have a step size, but most toolkit sliders do. This is an advantage that may give you pause for thought when redesigning a stand-alone GUI for a Pd patch.
And there's no easy way to represent graphs for arrays on a peripheral GUI. This opens a whole can of worms about good GUI design and decoupling. You either end up with a potentially slow application that shovels loads of data about when you update something, or you break good practice by calculating display code inside your GUI. There's no magic bullet. I tend to avoid fancy things like envelope graphs, meters and so on when making a remote GUI.