It depends on the cost/benefit ratio.

Looking at Nairobi to Mombasa as an example, it looks like Nairobi to Kyumvi and Makindu to Mombasa could be designed and built as high speed rail as the terrain looks relatively flat.

However, there is a set of hills between Kyumvi and Makindu that will make the geometry of the rail a lot trickier. The cost of viaducts and tunneling through those hills could be significantly more costly than the rest of the project combined. For the expensive part of the rail, it may be better to build that part at a lower design speed that can get upgraded later.

China built a great high speed rail system, but a lot of people in China still use the traditional rail system due to ticket cost, and the population in China is wealthier than the average African. You also have the African rail system being designed to operate with freight, which is something that the Chinese high speed rail network wasn't really designed to handle as much of.

The economics don't seem to favor high speed rail now, so it may be better to design the system so that it doesn't preclude high speed rail in the future.