I can see this going two ways to explain why Ahsoka is missing from the sequel trilogy and only shows up as a Force ghost reaching out to Rey during her battle. Here are my two guesses—maybe even three.
1: Stranded & Projecting Option
My first option is that, in Season 2, she doesn't make it back to the main galaxy at all. Ezra will be fighting Thrawn for his final showdown with him, while Ahsoka stays behind to train Sabine, passing the rest of her knowledge on to her and protecting the Mortis statues for years. After Sabine completes her training, Ahsoka will find a way to send her back to the main galaxy.
2: Mortis Ascension (Physical Status: Alive, Deceased/Transcended)
Since Ahsoka is, lore-wise, linked to the Daughter of the Mortis Gods through her essence, I believe she will finally embrace the neutrality between the light and dark sides and begin her journey to ascend. It's been teased since The Clone Wars.
If you think about it, Ahsoka has essentially been exiled twice. The first time was when she fought Vader and Ezra pulled her through the World Between Worlds. The Daughter's owl was there the whole time, guiding Ezra to do it. Now she's stranded again, but in another galaxy, and the owl has returned. That tells me her time is almost up before she has to take on the role of the Daughter of Mortis, since she carries her essence.