Because it's per unit of time. The faster you go, the higher throughput you'll have.

The frequency already accounts for the time component.

(People/Car)*(Car/Hour) = (People/Hour) = Throughput

At a constant frequency and higher speeds, you will simply have less trains on the track at the same time.

Yes, I guess you're right, but the maximum frequency is bounded by vehicle length and speed (you can't have a vehicle pass every thirty seconds if it takes more than thirty seconds for a single vehicle to pass a given point).

The longest TGV and Shinkansen consists are around 400 m, so they pass a given point in 30 seconds at about 50 km/h (30 mph). Of course there's spacing for safety and so on, but 50 km/h is so low that it's really a factor in practice unless you also have non-HSR traffic on the line.

A bigger factor in practical capacity is loading and offloading people and switching near termini.