The difference in the number of artifacts you see right after the import to your new instance is due to the fact that Artifactory exports do not include the cached items generated by virtual repositories (such as pom files). This explains why the artifact count in the new instance might be lower than in the original instance.
Also, it is possible that during your migration process, you did not export the artifacts in your remote repositories cache. No artifacts in your local repositories have been lost, and these artifacts will be re-cached upon download.
Another alternative is that Garbage Collection occurred between the time of which you have exported your previous instance and after the time you viewed the artifact count in your new instance.
So this situation is normal and no data should have been lost during your upgrade; however, if you want to be certain of this, you can check the logs for any errors/warnings during the import. Another way to verify that nothing was lost in transfer is to run the File List REST query on a repository in both instances and compare the results.