How does Safari manage its cookies?

I recently realised that Safari in iOS manages cookie separately for Safari.app and other apps that embed UIWebViews. I concluded so because I developed browser based app and saw the following behaviour:

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• login to web service which then sets session id to cookie.
• when I go to safari app and access the web service, I was asked to log in again.

Is it true that Safari in iOS manages cookie separately for safari app and other browser based app?

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Yes, you are correct.

Every app is sandboxed, meaning is has no access to any other app (which Mobile Safari is).

Thus, cookies set in a browser-based app will not affect the Mobile Safari app.

See this question for a possible workaround (kinda): Setting a cookie in an iPhone App

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It looks like you are trying to track your mobile app installations. I would recommend checking out yoz.io because they are free and do not require an sdk.

Enjoy ;)