We added this 16 Mhz crystal for customers who wished to use a crystal with their BBB or breadboard/homebrew Arduino. The space for the crystal and pads on the bottom of the board for the required load capacitors were added some time ago.
We provide both through-hole and surface-mount capacitors for the crystal’s load capacitance. Only two capacitors are required so you can afford to lose one while you’re soldering them on. For those experiments and hobbyists who have never done surface mount soldering, here’s your chance to start, since you only have to put on two capacitors. Surface mount (SM) soldering can be really useful, especially if a through-hole board has one or two tiny SM parts.