It has nothing to do with your indexes needed to be rebuilt or such.
Back in 8.2 this also happened. It's somewhat explainable why this is occurring. The Experience Analytics show every contact and interaction, because you are interested in value and overall profiling of your websites, products and pages. Because this is being processed for reporting purposes this doesn't take that much time to query upon.
If you take a look at the Experience Profiles than "they" suggest you are only interested in contacts that are known. These known contacts are identifiable by an identifier of your choice. You could in this case be only interested in these known contacts. While they aren't anonymous anymore they are processed and added/updated in the index/collection where they are stored. The Experience Profile uses this index/collection heavilly why browsing/searching through your contacts. Also the idenfication process to identify contacts uses these contacts of course.
If you really would like to have your anonymous contacts available in that index/collection than you need to patch that configuration. For Sitecore 9 this is put in the XConnect side of Sitecore. For Sitecore 8.2 this was part of ContentSearch.
Provides default configuration for component services for the application
When registering a type you can configure the following values:
Type (Required): The full type reference of the instance being registered
As (Optional): The type the instance may be resolved as (defaults to Type if not provided)
LifeTime (Optional): The lifetime of instance. Can be Singleton or Transient. (defaults to Singleton)
Options (Optional): If the type contains a constuctor that recieves IConfiguration, you can proivide
addtional values here to match the resulting type of options for that type.
<!-- SearchIndexer role requires Collection and CollectionSearch role services -->
<!--Enable ParallelizationDegree setting to override default value which is (processorCount*4)-->
And for Sitecore 8.2 this was configured differently.
<!-- CONTENT SEARCH - ANALYTICS - INDEX ANONYMOUS CONTACTS
This setting specifies whether anonymous contacts and their interactions are indexed.
If true, all contacts and all their interactions are indexed.
If false, only identified contacts and their interactions are indexed.
Default value: false
<setting name="ContentSearch.Analytics.IndexAnonymousContacts" value="false"/>
I hope you will get the point and let me know if this works for your solution!