Coming from a musical background (including extensive theory) before I played bass, note ID on the fretboard developed more in terms of intervals and patterns, more than note names for me. Once you know where a few fundamental notes are, you can easily extrapolate the rest of the board with time. I tend to learn the specific notes as I need them. Thinking in patterns/intervals:
I know that an octave is 2 stings down and two frets right. So if I know that E string, 5th fret is A, I know that D string 7th fret is the octave.
I know that 1 string down and 2 frets right is a fifth above. I know that that 1 string up, same fret is a fifth below.
To be clear, this is not a sight reading method - it's a take you time and flush thing out method.
Using this method, all you need to do is identify the notes on your lowest string and then extrapolate the other note values by interval. With time, you'll be easily able to identify notes all over the neck without all the thinking. Learn you intervals - especially bass critical intervals (3,4,5,6,7, octave) - and the rest will just come.