is this fast enough to catch the motherboard frequency???

It says it goes up to 5 MHz on digital signals. So it will measure the CPU clock of a 1981-model IBM Personal Computer. Today's fast PCs are about

A further problem is that as I understand it, in today's fast CPUs, the high-frequency clock signal exists only inside the CPU chip. It is multiplied from a lower-frequency signal outside. Am I remembering correctly?

Yep, internal clock frequency isn't the same as the bus frequency from the cpu to the outside world. You're a little behind the times at 2.5GHz, however. The latest desktop Pentium 4, for example, has a 3.8GHz clock.