Right, the 2 NIC ports are for either convenience or for more complicated networks that need to connect SSIDs to different VLANs / network segments that are physically tagged at the switch port, or something like that.
Basically, the only best practice to care for here is just making sure on the lower end AP's that you plug into a gigabit port instead of the 100mbit port.
And before the R710, you really don't need LACP / bonding, as Mitchell explained, the circumstances that lead to wifi throughput over a gigabit are often contrived and unrealistic. Even with the R710, that requires highly loaded and ideal clients on both 2.4GHz and 5GHz, which is still unlikely to happen consistently.
This is a great Rucks document discussing gigabit wifi: http://a030f85c1e25003d7609-b98377aee968aad08453374eb1df3398.r40.cf2.rackcdn.com/wp/wp-802.11ac.pdf
Namely, "Page 6" covers the math behind what the true throughput is of "1750mbit" gigabit wifi.