Can you think of any baseball products produced since 1994 that didn't have Jeter in it? Didn't think so. Jeter has not only been the face of Baseball since his inception but he's been the face of our Hobby.
Being this is his last full year in the majors, does this mean it will be the last we'll see of him in our cardboard world? Not even close. Typically you won't see "freshly" retired players in the following year products unless they are inserted as a subset, insert or variation of some sort. Even at that, you need to be a superstar in order to crack the mold on getting in. If you don't fall into this category you'll find these players coming back after 3-5 years of being away from the game in a Legends or Retro product.
Jeter won't be the same. With the legacy that he is leaving he'll be in a lot of sets in the foreseeable future. Now you might not see him as a regular base card player or normal current player inserts/subsets but I'm sure we'll be seeing one if not more Jeter type special inserts or subsets celebrating his career. The given Topps sets he'll be always apart of are Archives, Allen & Ginter, Gypsy Queen, Five Star, Tier One, Triple Threads, Museum and Tribute due to the product flavor of adding retired stars into the checklists. With Panini, they could include him in all of their releases since they have a mixed flavor of current and retired stars in each product they produce.
If you’re a Jeter collector it's a little saddening to have your player retired and not playing everyday. It takes some time to get use to it, however you will be still able to collect everything and anything of Jeter for a very long time. Sure it will be weird not seeing Jeter on the Topps Series 1 checklist for the first time but we'll see him everywhere else that you'll convince yourself he's still playing even though the box score is missing his name.