Yes, if the wax rings MIGHT be leaking, you should replace them asap. I have seen many people who sat down and the next thing they knew they were sitting with their pants around their ankles in their crawlspace because the leaking wax seal rotted the floor under the toilet!
As far as the water hammer, it is usually caused by a solenoid activated valve on a dishwasher or washing machine, or an overzealous 5 year old turning off the lever faucet in the bathroom.
Installing the air trap water hammer arrestors is usually effective, even if they "water log" after a while, they don't cost all that much to replace.
Call a plumber to come out and pay him to look at your system and give you some suggestions you can do yourself, and a bid for the stuff you don't want to tackle. DIY plumbing is fun until you go on vacation and come back to a hardwood floor 3 inches deep in hot water.