There are a few reasons for this, some involve training and others more economic. I'll add my two cents:
From a training standpoint:
1) after the primary early morning workout, many athletes (including mine) do group exercises, core work, and stretching, then will go into their easy (pole pole) run, often at a shuffle pace up to about 15km
2) after the second run, this gives their legs/body about 19 hours of recovery time, as opposed to about 13 if they run their second run later in the day
3) during months Oct - Jan it rains most afternoons, and Kenyans won't/don't run if it's raining
From an economic standpoint:
1) due to the communal effort by all to involve cooking and cleaning, it makes sense for them to enjoy a very light snack at the morning hard run, such as tea with too much sugar dumped in it and some fruit or maybe a piece of bread; after run #2 they can prepare a good lunch and in the afternoon after nap time, have time to prepare their big meal of the day with ugali and vegetables and sometimes fish or meat
2) fresh water is a commodity; at many camps water is still collected from a nearby river or stream, and this water is used for both showering and drinking (by way of adding chlorine) and cooking. Thus, there are no need for showing after run #1 as they go right into their exercises and other activities prior to run #2, so this saves a lot on water usage
As an aside, I manage 3 Kenyan guys and 2 ladies, from 4 different camps, and this is fairly commonplace as to their daily routines and structure.