First, two points about hole / barrel fill are: * A filled hole is an excellent indicator of the optimum process and optimum quality PCB. * The study that showed that holes need not be filled was paid for by the US Army and performed by Lockheed in New Jersey: Gangemi, R. and P. Cipolleti, "The Dynamic Measurement and Functional Inspection of Solder Joints", Picatinny Arsenal Technical Report No. 5055, December 1976. Available as AD-A034852 from National Technical Information Service, Springfield, VA.
Second, search the fine SMTnet Archives for background discussions.
Third, poor barrel fill in wave soldered PTH connections has a wide variety of causes. For starters: * Components: You mention ceramic capacitors. Have you checked the solderability of these components? * Boards: Cracked or poor barrel plating will limit barrel fill. How thick is your copper? * Process: Dwell and proper fluxing are key drivers to barrel fill. How long is your dwell? How do you know you are applying flux properly? * Materials: Have you checked your flux activity?
Finally, your rework issues are similar to your wave soldering issues. * Cracked barrels will not fill. [Tricky operators sometimes will 'paint' solder over the poorly filled hole to improve appearance.] * Poor design / BIG thermal planes on the board will dissipate the heat from your soldering iron, causing operators to stay on the connection too long, causing barrell cracking, bla, bla, bla