PHP.ini things can not be defined via /usr/local/hestia/data/templates/web/php-fpm/*(it only for FPM), and such edits like disable_functions will be overwritten with user/webdomain rebuild or HestiaCP updates.
You can search at /usr/local/hestia/ to see *.sh scripts that forcing such disable_functions overwrites with sed.
@eris any chance to preserve disable_functions over any HestiaCP updates or config rubuilds? Post-install hooks?