And what are these missing modules?
There's a total of 12 of them, in groups of four, scattered around the top of the board. Maybe it's for the MSO models with 16 digital lines?
I think these may be connectors for a high-speed logic analyser connection and/or MICTOR connectors - they appear to be grouped in differential pairs.
As regards the moisture sealant, this will be to avoid leakage due to board contamination on the RTC crystal's high impedance connections.
On the same subject, here are a couple of pics indide my Agilent MSO6034A :