Marvel Studios and Marvel publishing are independent of each other. As long as a title sells, it will continue. The most recent estimated sales for Fantastic Four were 34,930 for April. That's not spectacular but still puts them in the top 100. Ultimate FF is not doing well at 23,316 so if it goes much lower it will probably not continue after this first arc is done. With an unknown artist and 4 different inkers on the most recent issue of Ultimate FF, it doesn't appear that Marvel has the resources to really devote to this title to make it stand out. That is unfortunate because the writing has been pretty good so far.
I admit I was surprised that the first cover released for that 75th anniversary issue doesn't include the Fantastic Four. There will probably be variant covers that will include them.