european patent, page-19

However, I often wonder what the sp would be sitting at today if the market was privy to all information protected by these confidentially agreements?

Could be higher or could be lower. I am a big believer in inside information, even more so in these types of situations, so I don't necesarily expect confidential arrangements will undermine the shareprice of a stock. Speculation of what might be in confidential agreements can also push share prices higher. So you could argue either way. Saying that, it can also be very difficult to gain important institutional support when you don't divulge anything at all across any of your projects.