We have a client application connected to Modeshape; every communication is implemented trough the content repository api JCR. Modeshape implementation was initially 3.8.1.Final, and a migration to Modeshape 5.3.0.Final was successfully performed using a custom tool.
The file system nodes (folders) have custom properties; more specifically, a cf:FolderId property was defined to identify a ‘folder id’ which has the purpose to allow a folder lookup by id.
The folder search is performed via a JCR-SQL2 Query Language lookup:

SELECT * FROM [nt:folder]
WHERE (ISSAMENODE([nt:folder], ' /803F1481-D99D-11E7-A25F-988C20524153') OR ISDESCENDANTNODE([nt:folder], ' /803F1481-D99D-11E7-A25F-988C20524153 '))
AND [nt:folder].[cf:FolderId] = 'Root'

The base path ‘/803F1481-D99D-11E7-A25F-988C20524153’ identifies the root from which the query has to be executed and ‘Root’ identifies folder id. In other words, a lookup is performed, starting from base path /803F1481-D99D-11E7-A25F-988C20524153 searching for a folder which has a name ‘Root’.

In Modehsape 3.8.1.Final, lookup took just a few seconds; after migration to Modeshape 5.3.0.Final, lookup slowed down dramatically to more than 40 seconds and more.