Why don't large Decoupling/Bypass Caps use current limiting resistors?
Indeed, managing capacitor inrush current is a common challenge in electronic systems. Excessive inrush current can collapse supplies having high output impedance, trip fuses, cause output overshoot in regulators, and damage sensitive in-line components (usually semiconductors).

Personally, I've not heard of in-rush currents reducing the reliability of the capacitors themselves. Capacitors tend to be sensitive to over-voltage stresses, and suffer reduced reliability when exposed to chronic voltage stress. Current stress in a capacitor, on the other hand, is usually only a problem inasmuch as it generates heat. As long as the transient internal temperature rise during your hot-plug event is not enough to melt part of the capacitor, you are unlikely to observe an appreciable reduction in lifetime when turning on and off several times a day. You can find models for capacitor reliability that show the effect of chronic high temperatures (see here for example), estimate the temperature rise associated with your inrush event, and adjust for the duty cycle of your application (on the order of 2*1ms/day) to get a quantitative feel.

One application where in-rush control is important is server backplanes, where line cards are hot-plugged in to planes that are powering other, active loads. Not collapsing the source is key in this situation. There are IC products called "hot-swap controllers" that exist primarily to manage in-rush in this situation. You may glean some more insight by reading about hot-plug controllers.

As for bleed off resistors, they are only used in certain designs, especially where intrinsic safety is a concern or where the pins of the large capacitor may be exposed to other electronic systems (i.e. plug-and-play type situations).