PNachtwey,
I believe the capacitance of the hydrualic line is related to the stiffness of the line - just as an electrical capacitor stores charge/voltage, the hydraulic line stores pressure by expanding (like your cylinder). The line stiffness is related to the material (as well as diameter and wall thickness) of the pipe in question. This is basic pressure vessel stuff - I'll see if I can find a readily available reference for you on this. If the line has significant bends, etc then it gets more complicated. But for a basic tool a simple model should be sufficient as a starting point anyway.
For your GUI, you could have a range of picks for line models - like Schedule 40 steel pipe, SAE 100R, etc. Maybe as a first cut, you could also offer a "rigid line" or "ignore line capacitance effects" pick.
I agree that from a control systems standpoint the circuit can be simplified to a first or second order block, but what is more useful for hydraulic designers is to leave the details of the components in. The power of the Automation Studio or BathFP or tools like it is that it allows the designer to see the effect of swapping in new parts - not a 4-digit accuracy prediction of what happens, just enough to know if you're on the right track.
I teach at a technical college in the Toronto area, we use Parker stations to run experiments on - the biggest limitation I find is not being able to load the circuit...