The map in Subnautica is fixed in terms of the overall layout of the biomes, major landmarks, and key structures (like the Aurora, islands, and the Primary Containment Facility.) This is constant across all playthroughs. However, there are several elements within the game that have some variability:
Lifepod Spawn Location
While the lifepod will always spawn in the Safe Shallows, its exact location varies within this biome. This slight variation can affect your initial surroundings and proximity to other biomes. In fact, players have cited favorite spawn locations (mine is above the large coral tubes because they contain a lot of glass.)
Resources and Fragment Distribution
Wrecks also have a fixed location, but the specific fragments and resources you find within them are subject to some randomness. This means the exact layout of items you encounter can change between playthroughs, affecting your scavenging experience. Before I noticed that fragments were distributed differently, I experienced some frustration finding specific fragments on my second playthrough.
Updates and Game Versions
There have not been major map changes since the full release of Subnautica. However, after some updates, I did notice some minorly adjusted layout. Also, IIRC, the interior of the Aurora seems to have changed considerably. I must stress that this is related to updates. If you played during early access and then again post-release and after subsequent updates, these changes might be noticeable.
Minor Details
Within biomes, certain environmental features (like thermal vents or specific types of terrain) might appear slightly different due to some procedural generation of minor details.