Oh, I found out I was missing some configuration.
So first I need to install flatpak, like their docs say.
guix install flatpak
flatpak --user remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
Then to install apps, I need to run this. The --user flag is important.
flatpak install --user flathub com.logseq.Logseq
You also need to update XDG_DATA_HOME so that it includes Flatpak directories. There is a file Flatpak provides that can do this. The file is located at ~/.guix-profile/etc/profile.d/flatpak.sh. You need to run the commands in flatpak.sh. There’s a bunch of ways of doing this.
I decided to copy the contents of flatpak.sh into my ~/.bash_profile. Apparently, GDM (or GNOME?) reads this file when you’re logging in.
However, I didn’t copy flatpak.sh by hand. I used guix home of course. Here’s what my home.scm file looks like.
(use-modules (gnu home)
(gnu home services shells)
(guix gexp)
(gnu services))
(home-environment
(services
(list
(service home-bash-service-type
(home-bash-configuration
(bash-profile (list (local-file
(string-append (getenv "HOME") "/.guix-profile/etc/profile.d/flatpak.sh")
"flatpak.sh")))))
)))
Alternatively, you can extend ~/.profile, instead of using ~/.bash_profile.
(use-modules (gnu home)
(gnu home services shells)
(guix gexp)
(gnu services))
(home-environment
(services
(list
(simple-service 'flatpak-service
home-shell-profile-service-type
(list (local-file
(string-append (getenv "HOME") "/.guix-profile/etc/profile.d/flatpak.sh")
"flatpak.sh"))))))
Then I ran guix home reconfigure home.scm and rebooted my system just to be sure.
After all of that, the Flatpak apps now appear in GNOME’s app launcher! 
The only thing left to address is running the GNOME Software Center GUI app… aaand this I’m not sure about. The original Flatpak link says:
Note: graphical installation of Flatpak apps may not be possible with GNU Guix.
So… maybe this isn’t possible now? I’m totally fine with using install --user to install apps.