The reflection is heavily dependent on frequency. The ionosphere does attenuate or redlect short wave up to 30 MHz, but the Apollo missions used S band radio around 2 GHz, quite a bit above the plasma frequency, which is a few MHz for the ionosphere, and thus pretty transparent.
It's the reason why can pick up short wave radio stations from another continent, and why it doesn't work with UHF or above, and why satellite communication to ground all works with higher frequencies.
Yes, HF wouldn't have worked. But they didn't use HF, so there's that.
They used line of sight and high gain parabolic antennas for communication.
/edit: This is, btw., also the reason why Sputnik 1 sent its radio ping at 20 MHz and 40 MHz and not at lower frequencies, because the critical frequency below which there would be too much attenuation was estimated to be around 15 MHz depending on conditions. 20 MHz was still possible to be received by amateur radio equipment (and in particular a specific soviet direction finder system), and the signal was received by thousands of amateur radios up 10000 km away. That was a small radio transmitter with simple antennas. Apollo used much higher frequencies, high gain antennas, and higher transmitter powers to get enough bandwidth from 300000 km away.