In SugarCRM, the cache directory isn't used for just cached data. Let us look at a typical cache directory (5.0.0b, upgraded from Sugar 4.5.1):'

450_post_install_fix_backups
dashlets
diagnostic
dyn_lay
images
jsLanguage
modules
smarty
xml
blowfish
custom_fields
data
dynamic_fields
feeds
import
layout
pdf
upload

You cannot safely remove this directory from Sugar. Directories like '450_post_install_fix_backups', 'custom_fields' and 'upload' contain valuable, original files, which are in absolutely no way a cached version of whatever other file. If you remove this, you will lose data, and possibly, Sugar will stop working altogether.

My guess is, that Sugar was created with a cache directory for cache data only and, at some point, someone decided to store backup information and documents in it.

Always use the Administration module to clear out cached files.