I do not use AceFTP, but I am sure the following instructions provided by the makers of AceFTP on their site will make sense to AceFTP users.
How to ask AceFTP to show me hidden files? This configuration is in each site properties. Go in the properties of your site, in the GENERAL tab... you'll see a line named "Listing parameter", check the box to Override ancestor's values.... then check the line "Show hidden files".
Just below that, also check the line "Hide files beginning with a .", and uncheck the "Enabled" line below.
All the best,