Based on the information I received from someone who knows fenced stuff well, db2 reads this file in order to find who the owner of db2fmp process is. So, there should not be any impact to routines running as fenced.
However, I found the following mentioned here:
Backup and restore SQL schemas for DB2 Universal Database
"The procedures use the SYSPROC.ADMIN_CMD() stored procedure to export and the SYSPROC.DB2LOAD() stored procedure to load. (SYSPROC.ADMIN_CMD() has been introduced in DB2 V8.2.2 (FP 9). Therefore, V8.2.2 is the minimum version requirement.) SYSPROC.ADMIN_CMD() executes under the fenced user id and group specified by the owner of the sqllib\adm\.fenced file. As a result the exported files have the same owner and group as sqllib\adm\.fenced. Therefore it is important to ensure that the user or group has privileges to write to the specified directories, while the user id expected to access the files also has access. The simple solution is to change ownership of sqllib\adm\.fenced to the instance owner. The safer solution is to have both IDs as members of a shared group and change only the group ownership of sqllib\adm\.fenced to that shared group. This way it is ensured that you can access the produced files through the group membership."