It wont work like that, unless you play your CCM with the option of pre-existing injuries on. If you play your CCM with pre-existing injuries on, then yes, any player that was put on IR in time for the roster update, will indeed be on IR. You will still have those players in the game, but with them being on IR, you cant use them until the following season of your CCM. If you play with pre-existing injuries off (which I assume most people do, as do I), then injured players will be on the teams without their injuries. Regardless, Jeff Demps and the many other players who have been IRed in real life will be in the game.
When you see "removed from depth chart due to suspension", it doesnt mean that they have been removed from the game completely. It just means that they've been taken off the depth chart as a starter.
Use Joe Haden as an example. There are 5 corner back spots on the depth chart...Donny Moore (the so called ratings czar) just removed him from being listed on any of those 5 corner back spots on the depth chart, to reflect him being suspended. But regardless, if you play a play now or online game, you can just manually put him back on to one of the 5 corner back spots on the depth chart yourself. When you start a CCM, this will not be an issue, since you'll be starting fresh and can adjust your depth chart to your liking.
Hope this makes sense and clears everything up for ya.