You are correct that hand soldering ceramic capacitors often causes them to crack. They do not take thermal shock well. You might be able to reduce the amount of cracking by following the rework repair guidelines discussed in the fine SMTnet Archives. Addirtionally, many ceramic capacitor suppliers provide guidelines for soldering their products.
Your boards sound like the board equivalent of a root canal. If a contractor refuses your product, that's really bad. Those guys will try to build anything. Comments are: * Put PTH on only one side * Put complex SMT on the PTH side, less complex SMT on any side it wants to go * Attach SMT, PTH next, and hardware last
If you continue to allow your designers to do any pinhead thing that pleases them, your boards will continue to be unmanufacturable. Design/Layout rules: * IPC-2221 * IPC-2222
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