The great thing about a PDC for calming the citizens is that the population only cares about the total HS devoted to beam weapons and missile launchers. Slapping a set of ICBM launchers along side a modern missile fire control is a cheap way to keep people happy (even if it is of minimal military utility)
As for generic missile tips...
• Design a 0.1MSP 'PlaceHolder' engine at 1/2 of your maximum missile engine power. The placeholder is a great way to mess around in the missile design window to keep a feel for range (about equal if 2.0-3.0 total engine size) and speed (double). Design a new engine of the total size at maximum power when you have something you like.
• Your anti-ship missiles should probably be 30-40% warhead, 50-60% engine, and 1-20% fuel/armor/sensors/agility/ect
• For optimal damage the warhead should be the square of a number (1,4,9,16...), or at least a half step (2,6,12,20...). Everything else has a damage template that is skewed toward shallow penetration.
• Smaller missile can more easily penetrate missile defenses. Larger missiles have longer ranges. Size 4-5 is one of the most popular size ranges.
• In the early game I consider a 1-HS M-FC (3-HS Active) as short ranged; a 2-HS M-FC (6-HS Active) as medium ranged, and a 3-HS M-FC (9-HS Active) as long ranged. If cost is no limit going larger is often better.