When you see an input circuit like the one Intronix used for the voltage offset, you know that it was designed by by some poor engineer who spent a month or two juggling with board layouts, resistor values and resistor configurations until the best overall performance was achieved. You know they spent a lot of time on this as getting the signal from the test board to the Altera input pins with the offset adjustment is the most critical part of the hardware design. The Logicport can work at higher frequencies then most of their competitors, and this input circuit and board layout is the key.
I would say the resistors at each end of the transmission lines are there to dampen ringing, but I couldn't tell you if the motivation for the 100 ohms was for better signal integrity on the input pins, limiting the peak current into the Altera input protection diodes to a level that allows the diodes to recover in nanoseconds even with transmission lines that are not properly terminated, or just to stop the transmission lines ringing like a bell. In circuits like this, you put the absolute minimum in that you can get away with, and this through testing proved to be the absolute minimum.
It may be one of those things that Intronix says that they are not completely sure why it works, but it does.
The only ESD protection is the protection built into the Altera inputs, and that is also used for clipping when the input exceeds the Altera input voltage range.
Devices like this are handled with the same ESD care as the board under test, so they would never add protection to a 4.7pF capacitor. It would be 500V rating, and with a 150K resistor in parallel you would need over 3mA of ESD current just to reach that 500V. If you are exposing the analyzer to that much ESD energy, then forget it - find a new job.
Richard