How do I embed an Ionic webapp?
The problem probably is you have two .htaccess files rewriting URLs to index.php (Drupal) or index.html (Ionic). I think you need to adjust Drupal's rewrite rule because it is in the top level:
  # Pass all requests not referring directly to files in the filesystem to
  # index.php.
  RewriteCond %{REQUEST_FILENAME} !-f
  RewriteCond %{REQUEST_FILENAME} !-d
  RewriteCond %{REQUEST_URI} !=/favicon.ico
  RewriteRule ^ index.php [L]

For example by adding this condition:
RewriteCond %{REQUEST_URI} !^/webapp