Your first two photos are of the hardened UHF antenna which in the Atlas era would have been used to communicate with the helicopters transporting crews/security forces as well as for receiving force direction messages from SAC & emergency action messages from JCS, via airborne command post. Minuteman sites had a similar antenna for the same purposes, but it would also be used to communicate on GIANT STAR -- SAC's UHF SATCOM network (244MHz downlinks).
The VHF tower would have been to communicate with all the personnel at the site, & in some cases they also used VHF radio as a redundant means to communicate with other nearby sites & the main base (Plattsburgh AFB) as well as ground transport vehicles in the area.
The Atlas sites were only in operation for about 5 years, all being deactivated by the end of 1965, so the comms were fairly low-tech, and HF/SSB was one of the most important systems for command & control.
Seems like with *some* Atlas Wings, all of the sites had soft HF antennas in addition to the hardened, tx & rx antenna systems. With others, they just had two hardened HF tx antennas in one 'can' underground & then deliberately located further away in the compound there'd be a separate 'can' storing I think 5 HF rx antennas. Receiving was much more important than transmitting at the sites. Depending on the readiness condition protocols, they may just use a soft HF antenna to receive traffic, or if on a higher state of alert they may raise one telescoping HF rx antenna out of the hardened pod, with or without also raising one hardened tx antenna up. If those antennas got destroyed by enemy attack, they had the one other HF tx antenna they could raise, & several other HF rx antennas they could raise (one at a time).
The key concern was & still-is redundancy. Many sites had a soft or hard microwave radio link that'd link all the missile sites plus their main base -- as long as orders were received in the proper format and authenticated, it didn't matter if the orders were received via telephone, or HF/SSB, though the reality is operational orders would have been sent & received by multiple links.
As far as truly "underground" antennas, the more modern missile alert facilities had one for the survivable low frequency communications system, and then a select number of sites had the Sylvania Ground Electronics System which utilized a buried mediumwave antenna to establish a link with the launch facilities.
By the late 1980s, improved technology & redundancy caused SAC to phase-out the HF/SSB use at most Minuteman missile alert facilities. Soft antennas were mostly removed but the hardened tx & rx antennas were retired in-place. I believe the missile alert facilities that operated as Squadron Command Posts retained the soft HF & at least the hardened tx antennas for a while longer.
I used to hear at least one SAC Strategic Missile Wing -- I think Minuteman, not Titan II -- on 11494USB back in the early & mid-1980s doing what to me at the time, sounded like routine training with the hardened tx & rx antennas.
There are plenty of old US Army Corps of Engineers blueprints available which will show the exact layouts of the old Atlas & Titan sites (Minuteman sites were a lot more standardized).
