I've also seen apps disappear when installing tweaks that control or otherwise modify springboard's layout.
I'd try:
0) Uninstalling/reinstalling that tweak you just installed.
1) Verifying they're in Cydia & Spotlight.
2) Verify no tweaks are hiding the apps in question.
3) If the dock is hidden, unhide it and check it for the missing apps.
3) Check Safe Mode for the app icons.