If there is any krausen it is impossible to read the hydrometer. That being said, if you are taking your FG reading I am assuming you are getting ready to bottle/keg, so why not just draw off a sample and measure it in your tube? Or if you are transferring to a secondary, grab some from the siphon tube. I use buckets with spigots so taking readings is fairly easy.
That being said, it the top of the brew is free of crud and you don't want to draw any off, then go for it. I would just say don't do it like that too much as removing the lid will introduce oxygen to the head space. Find what works best for you, play around with it.