According to PokemonGO Hub, a global reshuffle of Pokemon spawn-points in Pokemon GO is to blame for various disappearing Pokemon you may have witnessed in-game over the last day or so.
While neither Niantic nor the Pokemon Company have shared information on the change, this is not unusual as they rarely talk about the ways the game decides to spawn Pokemon in certain areas. I get the feeling this may be one of those times when gamers prefer not to know to see how the sausage is made, so that might be a good thing.
The good folks at PokemonGO Hub have done a lot of work figuring out what went on, however. The first thing they were able to confirm is that the change is indeed global. After reaching out to their community, and the Pokemon GO community at large, they were able to verify that these changes appear to be happening everywhere.
Change include new spawn points in densely populated areas and removed from areas with lower activity. Some spawn clusters (groups of spawn points) appear to have been reduced in size, while others were increased in size.
For full details on what they discovered, I strongly advise you to read their article on the subject. For now, you can take their discoveries as a reason for any strange spawning behavior or glitches you have noticed in the game recently. If the way Pokemon GO feels, about Pokemon population, has changed for you, then it seems that a global reshuffle is a reason why.