Marvel and Disney have done an awful lot to try and halt 20th Century Fox's success when it comes to the X-Men universe. Deadpool's fate is also tied to that, so when they decided to kill him off in the comics, you know Ryan Reynolds had to get in on that action.
Reynolds, playing Deadpool in the 2016 film, has (from what we can see) stayed very true to the comic book character. Unfortunately for him, he's part of a 20th Century Fox Marvel project, and they won't be helping him in any way.
Marvel has done a lot to try and take these characters away from their universe. They don't want to give Fox anything to go on. So they're ending Fantastic Four, killed off Wolverine, and now Deadpool.
I don't know if it will have a negative effect on the films, but you can bet Marvel hopes it does.