The real reason is that it would cost money.
http://fridaythe13thfilms.com/blog/dani ... ditions-2/"There was some discussion about adding the lost scenes (especially in Part 4) back into the picture, but there are a slew of legal issues surrounding a revised version. It mainly has to do with the guilds — the Writers Guild and Directors Guild — who have strict rules about making changes to director’s and writer’s work. That said, of course there could be a way to create a new or alternate version if the director and writer were to come to terms with the studio, but that is a long road and we honestly thought it would be best to show fans all of the trimmed gore sequences with multiple angles and director commentary than trying to reinsert pieces of these trims into the actual film."
The film business works differently than many others and you can't just do a re-cut of a film because you have all of the parts. The reason for this is that re-cutting the film constitutes a new version of the film.
Thus, dropping deleted scenes in as special features cost nothing but reintegrating them into the full film would be a substantial cost.
The only reason the first film was done this way was that it was not a modern re-cutting of the film (such as doing any of the sequels would be.) All they did was take the European version that was released circa thirty years ago and released it over here as a 'unrated' version. Which, to be honest, Sean has stated that very little was ever cut or left out of the first Friday the 13Th because they were on a tight schedule and budget and just didn't have to time to film hardly anything more than what was absolutely necessary. What we see in the European Edition aka the Deluxe Edition, is considered to be the fully restored film by most people. And I see little reason to doubt that this is true.
Newline did a similar thing with Part 9. The 'unrated' version on the DVD was nothing more than the European version. As such, that is why we don't see the original ending or other deleted scenes; such as the fully grown Hell Baby reintegrated into the film. That would constitute a new cut of the film, and Newline would have had to spend more money.