My contacts are disappearing on their own
In my personal experience, the issue might be an iCloud syncing problem or somehow the main group in your Contacts app has been unselected.
To check to see if all of your Contact groups are selected, open the Contacts app and tap on the groups button on the top left corner.  You should see a checkmark next to the groups that are selected.
If this is not the issue, then you might want to go to iCloud.com to see if your contacts are at least stored on the cloud.
To answer your last question, yes there is a chance that something malicious could be occurring but it is very improbable unless someone managed to hack your Apple ID.