The current GUI only allows the exclusion of individual folders, not all folders called e.g. .svn
But there is an advanced way of adding exclusions - see
https://help.backblaze.com/hc/en-us/articles/220973007-Advanced-Topic-Setting-Custom-Exclusions-via-XML
As an example, I added the following rule to exclude .git hidden folders, only if they were in my ~/Sites folder (another similar could apply to .svn, node_modules etc.):
<excludefname_rule plat="mac" osVers="*" ruleIsOptional="t" skipFirstCharThenStartsWith="users/" contains_1="/sites/" contains_2="/.git/" doesNotContain="*" endsWith="*" hasFileExtension="*" />