As far as the brakes feeling mushy, it really depends on what car you're coming from. If your last car was a modded mustang with upgraded brakes, then the stockers may feel a little soft. If you coming from a stock civic, then they definitely should not be soft.
As far as the parking brake goes..... as the brake pads wear, it will take more vertical force on the E brake lever for the same amount of brake force. 45k on a single set of pads, you may be ready for an upgrade, so that the e-brake isn't soft. More importantly, if the e-brake doesn't seem to engage as well as before, that most likely means that you rear brakes are functioning quite as well as they used to.... time to get them checked out or upgraded.
In the end, brake parts are relatively cheap. Just replace them and have the extra piece of mind. You may cheap out on the oil/antifreeze/gas that you put in the car, but one thing you should always spend money on is your brakes. Just remember, new pads and rotors (even performance ones) are MUCH cheaper than a trip to the body shop......