Search for files across multiple SharePoint site collections and their subsites

[James Curtis]

We have a custom .NET web application that will be connecting to SharePoint over SharePoint's API primarily to store documents in SharePoint and take advantage of the document management functionality like check-in/check-out, versioning, etc.

We will not be using the SharePoint UI at all.  The custom .NET web application is the only UI the user will see (SharePoint in the background for document storage). 

Question(s): Is there a way to search across all Site Collections and their subsites?  What is the process?

[#2]

Yes, you can use the search rest API
https://docs.microsoft.com/en-us/sharepoint/dev/general-development/sharepoint-search-rest-api-overv...

Search can crawl information from your entire tenant, so you shouldn't have problems by having multiple site collections