3.0 Exclusions
The Limited Warranty does not apply if the Hardware:
has been modified or repaired by anyone except a Valve-designated service center and the cause of the issue for which you seek service is the modification or repair, or damage caused by either;
Quote from Valve Hardware Warranty.
In other words, simply changing SSD doesn't void warranty, but damaging the Steam Deck in the process of doing so does.
They are absolutely brilliant!