are the apps being uninstalled during OS update?
If you do a normal system update (no restore or something like that) your apps are not uninstalled. The system doesn't really do anything with your apps at all until it finished the system update. Then the system will recompile all apps (The 'android is optimizing apps' dialog) in order to make them run faster. This should not interfere in any way with your data. 

I do not know about your specific problem with WhatsApp or if a system update could cause your error but your data will not be touched by the system during the update. This means if something breaks whatsapp your data will still exist in order to restore your history.

Btw. what android version are you running? With android 7 the recompile step will partially change (to the good).