Caps missing on a logic board, compared to board layout?

There are a lot of empty pads in the RF area of the iPhone. The way to know if something should be there or not is the presence of a small dome of solder on the pads. When there is a dome of solder, then no component was ever there. If you see a shiny, flat pad, then there was probably a component there before being dislodged.

When your unsure, then consult the schematic for the proper component and see if it says NO STUFF. That indicates that the component should not be present on the logic board, even if it is in the schematic. Those NO STUFF parts are usually there during the development of the board for diagnostic purposes but not necessary for the final version.