If your current WiFi card has 3 antenna connectors, it's probably because it is a higher-end card from the 802.11n era, where 3-antenna cards were popular.  Cards like the Intel 6300 worked this way.  In the 802.11ac world, 3-antenna cards are very rare.  The only laptops I know of that use 3-antenna 802.11ac cards are certain Apple laptops, and Apple uses Broadcom cards. Intel's top 802.11ac cards only use 2 antennas.  But yes, you can still use a 2-antenna card in your system; you would just leave one of the antennas disconnected.  I would recommend putting a small piece of electrical tape or plastic around the unused antenna connector to avoid any issues that might arise from allowing it to contact other surfaces.  When Dell ships systems that have 3 antennas preinstalled but a WiFi card that only uses 2 of them, they install a small plastic tube around the unused antenna.

The Latitude E6540 uses an mPCIe slot for its WiFi card, so the card I would recommend for you is the Intel Wireless-AC 7260HMW.  That was the best WiFi card Intel made in mPCIe format before everything switched to M.2/NGFF, and in my opinion the best WiFi card anyone made in that format.  It does support Bluetooth 4.0.  Make sure you get the Wireless-AC 7260, not the Wireless-N 7260 (I have no idea why Intel used the same model number for two completely different cards) and also make sure you get the 7260HMW, not the 7260NGW, since the NGW version is an M.2 card that your system won't accept.