We have build an app in which we have integrated the Sales Force mobile sdk for Android and iOS. We have integrated lightning pages in the app. Since the Mobile web experience is retired. Is there a way to access the lightning web pages in the native android and iOS apps
As an alternative, your users may use Lightning Experience (LEX) on iPad Browsers (Beta).
To answer your other question, Salesforce is not decommissioning the Salesforce App for iPad. Since Salesforce Mobile Web Experience is retiring, users now have the additional option of using Lightning Experience on iPad through Safari (mentioned right above), which was not available previously.
As far as the App view goes, as previously mentioned, if your users are viewing the Classic UI in the Salesforce mobile app on iPads, this is likely because you have not opted into Lightning on Mobile during the Winter '20 Release (https://help.salesforce.com/articleView?id=000352373&language=en_US&mode=1&type=1), in which case your users will be unable to see the new UI and will view the previous UI in the Salesforce mobile app on iPads and Android tablets (mobile devices were updated, but tablets were not).