It seems that the reported bug is still not resolved and you can not disable the Legacy File Manager from WHM without turning off the File Manager.
You can find more details about it at:
Bug 5584 - No way of removing "legacy file manager" from x3 cpanel
However, there is a workaround.
You can just disable the Legacy File Manager icon.
This can be done by editing the
/usr/local/cpanel/base/frontend/x3/dynamicui.conf file. If you are using a different theme, enter its name instead of
x3.
In the file, search for the following line:
description=>$LANG{'TFileManagerLegacy'},feature=>filemanager,file=>legacy_filemanager,group=>files,height=>32,imgtype=>icon,itemdesc=>$LANG{'TFileManagerLegacy'} ,subtype=>img,type=>image,url=>files/index.html?showhidden=1&dir=/public_html,width=>32,itemorder=>2,acontent=>target="_blank",onclick=>show_optionselect('files'); return false;,searchtext=>$LANG{'filemgrleg-searchtxt'}
Put the comment character in front of it. The new code will be:
#description=>$LANG{'TFileManagerLegacy'},feature=>filemanager,file=>legacy_filemanager,group=>files,height=>32,imgtype=>icon,itemdesc=>$LANG{'TFileManagerLegacy'} ,subtype=>img,type=>image,url=>files/index.html?showhidden=1&dir=/public_html,width=>32,itemorder=>2,acontent=>target="_blank",onclick=>show_optionselect('files'); return false;,searchtext=>$LANG{'filemgrleg-searchtxt'}
Save the file and open your cPanel. The Legacy File Manager icon will not be visible anymore.