I'm not sure how much information you'd get about the height - if the ship's rolling and you've just got this beam coming from nowhere how easy is it going to be to accurately judge the height of it? If their fire discipline is anything like Germans in WWI you're not going to have very long at all in which to make a judgement, too...
The point would not be to compare the absolute height (since you have no base reference), but the difference in height. If the foremast has a searchlight platform 15' higher than the mainmast's, and the light on the right side of your view is lower, then the ship is obviously presenting her port side to you and is likely passing right-to-left.
Not a huge detail, but it seems like you might want to put all lights at the same level in order to deny the enemy this information.
A bigger, more dangerous step might be to concentrate all searchlights at a single point on the ship, and have backup lights elsewhere in case the primary position is lost. In this way, you deny all azimuth information.