I would say it’s not recommended to rely on Cookies. It is not guaranteed that iOS and Android will keep them around. We use a Bearer token stored in Preferences with great success. See Best way to store Bearer token from API? - #2 by twestrick.
The most recent conversation about this is over here where a Capacitor team member says don’t use them for native 
- Cookies vs. Preferences - what is more persistent?.
Overall, if you search this forum for posts about cookies, there are a ton with people having problems.