I am building a device that will be controlled by several digital encoders, all which are hooked up to the device's Raspberry Pi 3 model B. I know this may be a trivial question but bear with me as I have never built a device using a RPi before, but can a single one of the 5V pins be used to power multiple digital encoders, or muxs, or other devices in the system that need 5V power? I was thinking put the 5V pin into a breadboard and be able to plug any device into connected pin holes that need power. The digital encoders require 5V power @ 30ma. And if they can be used to power multiple devices, what is the maximum amperage output of the 5V pins and 3.3V pins? Additionally, can these pins be deactivated while the RPi is on or do they always output a set voltage?
Yes, the 5V and 3V3 power rails may be used to power multiple devices.
The power rails are not switchable, power is always available while the Pi is powered.
The amount of power available from the 5V and 3V3 rails is determined by the amount of power you can feed in via the microUSB power socket (or via the 5V power rail if you are powering via the expansion header).
Different Pi models have different microUSB polyfuses which limit the current. You can use the residue of current after that needed to power the Pi and its peripherals.
Early model Pis have a limited amount of 3V3 power because of the chips used, perhaps only 50 mA or so. Later model Pis have upgraded chips and you may be able to draw 500 mA or so.
The Pi3 has a two amp polyfuse. Provided you have spare power you should be able to draw up to almost an amp from both the 5V and 3V3 power rails.
You don't specify which Pi, but for Pi3 You can draw 800mA from 3.3V and 1200mA (possibly more) from 5V, given an adequate power supply (2.5A).
The actual current depends on what else you have connected. If you are drawing lots from USB, the 5V would be correspondingly reduced.
Earlier models has lower capacity.
See Raspberry Pi Power Limitations for more detail.