SUMMARY
When I ran the skrooge flatpak in 2019-06, the console showed a warning
  ##WARNING: Audio notification requested, but sound file from notifyrc file was not found, aborting audio notification
and there are no sounds.
Searching for "flatpak" and this warning message suggests that the marble and kdenlive flatpaks also don't play notification sounds, but I haven't reproduced this problem with them.

STEPS TO REPRODUCE
1. flatpak install org.kde.skrooge
2. flatpak run org.kde.skrooge
3a Click Accounts, create an account (choose any bank icon, enter Account "test" and Number "1234" and click [+ Add]).
3b Open Settings > Notifications, choose a notification,  and click the [▶] play button.

OBSERVED RESULT
The following appeared at startup in the terminal:
  ##WARNING: Audio notification requested, but sound file from notifyrc file was not found, aborting audio notification
And when I performed operations that normally play a happy sound, there's no sound.

EXPECTED RESULT
No startup warning, and sounds.

skrooge.notifyrc specifies
  Sound=Oxygen-Sys-App-Error.ogg
  Sound=Oxygen-Sys-App-Negative.ogg
  Sound=Oxygen-Sys-App-Message.ogg
  Sound=Oxygen-Sys-App-Positive.ogg

strace showed the flatpak app tries to access these sounds from  
  $HOME/.var/app/org.kde.skrooge/data/sounds/
  /app/share/sounds/
  /usr/share/sounds/
  /run/host/share/sounds/
and they're not available in any location, hence the warning.

In Fedora, these files are in /usr/share/sounds/ , supplied by the oxygen-sound-theme package, so maybe that package should be part of the KDE Platform runtime the same way the Oxygen icons and the share/sounds/freedesktop/stereo/ files are; I filed bug 409300 against the Qt/KDE Flatpak Runtime project, from which I "forked" this bug against Skrooge.

SOFTWARE/OS VERSIONS
flatpak version 1.4.1
Linux/KDE Plasma: 
(available in About System)
^ from `flatpak run --command='kdeinit5' org.kde.Platform --version`
KDE Plasma Version: n/a
KDE Frameworks Version: 5.12.4
Qt Version: 5.59.0

ADDITIONAL INFORMATION
I retried this in 2020 recently with newer Flatpak 1.4.4 and runtimes, and came up with a workaround. If I 
a) copy these four Oxygen-Sys-App-* sound files either to the Skrooge flatpak app's data directory $HOME/.var/app/org.kde.skrooge/data/sounds/ or to the KDE Platform runtime directory /var/lib/flatpak/runtime/org.kde.Platform/x86_64/5.12/active/files/share/sounds
b) start Skrooge nightly with `flatpak run --socket=pulseaudio org.kde.skrooge`

then I hear sounds! If I only do a) skrooge prints
  AL lib: (EE) ALCplaybackOSS_open: Could not open /dev/dsp: No such file or directory
in the console.

To fix b) add
      "--socket=pulseaudio",
to "finish-args" in org.kde.skrooge.json. (FWIW this is already in Flathub's "recipe" https://github.com/flathub/org.kde.skrooge/blob/master/org.kde.skrooge.json .)

While waiting for some resolution to bug 409300 perhaps Skrooge could fix a) by incorporating these sound files somewhere in its flatpak build.