A lot of it's about fuel efficiency. Hovercraft are excellent as amphibious vehicles, and very fast, but they drink fuel like nothing else on Earth. Going faster with ships produces drag to the square of speed, thus making it more efficient to reduce top speed by a couple of knots when there is no competition. The same with Concorde, which had an excellent lift/drag ratio at supersonic speeds, giving about the same seat/mile costs as a 747. However, the problem was a terrible lift/drag ratio at low subsonic speeds, which resulted in a lot of fuel being burnt when flying slowly. The XB-70, which could lower its wingtips at supersonic speeds, had the best lift/drag ratio of any manned aircraft, and was much more efficient at subsonic speeds. Unfortunately, the design never made it into civilian service.
As for train speeds, increasing the top speed is not very helpful unless you spend ages at that speed. The thing we need to work on in Britain is acceleration, and we have been very good at that. I remember hearing stories of how 313s used to knock the spots of Deltics leaving King's Cross, but a Pendolino would leave almost any suburban unit standing with a similar comparison.