What it looks like is referring to what the ship looks like. How would be used if they were looking for a way to excavate the ship. The entire phrase would be different.
"He hopes to excavate making use of a new robot that uses sound to make a computer plan of the wreck, and in this way create an accurate picture of HOW the ship is laying or if it is stable, and to see how the seabed looks"
What = how it looks they are going to excavate anyway.
How = how is the situation can the ship be excavated?
So = very so the lights are very bright.
TOO bright would equal the lights are very bright, I don't think people would make a distinction they would use either word.
But grammatically so = the lights were intense and broke the law.
And too bright = more than needed but not breaking the law.
You can read about "so" and "too" here