.htaccess - Disadvantages

Disadvantages

Controlling Apache using the main server configuration file httpd.conf is often preferred for security and performance reasons:

Performance loss
For each HTTP request, there are additional file-system accesses for parent directories when using .htaccess, to check for possibly existing .htaccess files in those parent directories which are allowed to hold .htaccess files. It is possible to programatically migrate directives from .htaccess to httpd.conf if this performance loss is a concern.
Security
Allowing individual users to modify the configuration of a server can cause security concerns if not set up properly.

Read more about this topic:  .htaccess