An internal slideshow from Epic Games presented many promotional plans for the game that are planned for this year and beyond. This document, leaked from a recent lawsuit between Epic Games and Apple, features a selection of characters which they want to make skins of (including characters that were never mentioned until now). One of them is Samus Aran!
However, there is no way to know which elements of this document were scrapped, and which weren’t. Nintendo tends to be very protective of their IPs, so it is possible that they refused this collaboration. Then again, Rocket League does feature exclusive Samus, Mario and Luigi themed cars on its Switch version (they are seen as other car models in online crossplay). Samus making an appearance in Fortnite is definitely still possible, and Metroid could greatly benefit of the visibility given by such a popular game!
Source: The Verge