If you mean a hydraulic clutch and slave or a hydraulic throw out bearing, I don't use them. For clarity, those are actually two different set ups using a hydraulic reservoir.
I do have a hydraulic throw out bearing in an SVT Contour (son's car) and it is prone to leaking. It's not a good set up since any kind of servicing needs to have the transmission removed. There has been a kit for hydraulic throw out bearings for Panteras for 30 years. Same issues. Don't use them.
The stock mechanical linkage is appropriate for the car. The hydraulic system isn't.
I've heard stories that the hydraulic unit needs a very firm mount and the stock Mustang firewall isn't. It flexes and quickly fatigues and fractures.
I don't know how you would adapt a cable shifter to this application. I don't think that you need to worry so much about fitting in a shift lever.
I've got a stock Mustang lever on a Hurst mechanism. Lots can be done there.
PROBABLY the worst that will happen is that you need to alter the stock shifter boot ring spot welded to the floor. The space alotted to the shift lever opening by Ford is really tight. Something like 3-1/2 x 3-1/2".
I don't know of anyone who has done this swap that said they were sorry and wanted to go back. It's really something how the cars should have been built originally.
Like Nike says, just do it.