If you have three cities on a perfectly straight line, you can run your high-speed trains as above.
If the city in the middle is not on a straight line path between the two end cities, now your train tracks need to curve to connect the three. If you make the curve a large enough, smooth enough curve, it won't hurt your maximum speed much, but when you're talking "1000 km/hr" ... and in any case, you're also adding miles to your route, and if you make your route 20% longer to weave from city to city along the way, you are also make it 20% slower.
If you have three cities on a perfectly straight line, you can run your high-speed trains as above.
If the city in the middle is not on a straight line path between the two end cities, now your train tracks need to curve to connect the three. If you make the curve a large enough, smooth enough curve, it won't hurt your maximum speed much, but when you're talking "1000 km/hr" ... and in any case, you're also adding miles to your route, and if you make your route 20% longer to weave from city to city along the way, you are also make it 20% slower.