I am not familiar with chocolatey but the powershell script on https://chocolatey.org/packages/filezilla (click show files) contains the following
$url = "http://sourceforge.net/projects/filezilla/files/FileZilla_Client/${version}/FileZilla_${version}_win32-setup.exe/download"
$url64bit = "http://sourceforge.net/projects/filezilla/files/FileZilla_Client/${version}/FileZilla_${version}_win64-setup.exe/download"
So its still fetching executables from sourceforge using plain http with no checksums or signatures in sight. On the assumption that executable does include the sourceforge malware, The silent install argument ("/S") passed to the executable by chocolatey seems to be the only reason its not installed along with filezilla.Is there any reason to believe ninite does anything different?