As stated on the Trivia Pages for both characters, originally the writers for the Inferno arc had intended for Lara to come to realize that her feelings for Sam were romantic during her drug induced trip after eating a bit of the bark from the tree of life. However, for whatever reason, likely the higher ups Vetoing the scene because even after shows that have been huge hits with critics and audiance alike( like She-Ra and the Princesses of Power, The Legend of Korra, Adventure Time, Steven Universe and most recently Kipo and the Age of Wonderbeasts) it's still seen as a massive risk to pair to people of the same sex together in a major Triple A Game even if the pairing in question is the most popular in the fandom right now.
For the record, if you don't ship Lara and Sam that's perfectly fine, but the fact that Sam and her relationship with Lara has remained popular for 7 years that the rumor that Sam MIGHT appear in the upcoming sequel to the 2018 movie has caught the attention of several major news articles is significant. I mean, how many people talk about Lara's mother, who was a major player in the Legends Timeline and the very popular Blood Ties DLC from Rise. How many people fans are still talking about Zip, or even Jonah, who is the only character to have appeared in every game of the Survivor Timeline besides Lara.
Sam has remained popular despite her limited screen time and despite the studio trying to side line her and yet she keeps coming back and still is shipped with Lara to this day. And creators like Jackson Lanzing, Phillip Sevy and Gail Fricking Simone still go over how much fun it was to write and draw her. Sevy has even stated in the 20 Years of Tomb Raider that Sam was his favorite character to work on and stated that before he even had a chance to draw her he was sent tons of Email that was asking about her and what her fate would be.
And in Inferno the writers worked to get the Lara and Sam together romantically despite Sam being sidelined Again. Again, remaining in the fan popular consensus for 7 years is no small feet and with Tomb Raider I can only think of 3 characters not named Lara Croft who have remained in popular with fans, Winston, Jacqueline Natla and Sam Nishimura.
It'll be interesting to see how Sam's involvement in the series develops especially if/when I get my TR Animated Web Series done.