Yes its a subtle but important difference. At the risk of further advice on terminology, can you confirm you disabled Javascript rather than Java. Java is rarely used for anything and certainly not in Moodle.
Things that might cause a performance issue with javascript is if a resource (e.g. RSS or other block), is making a call to an external site which is horribly slow. Another example is if you have MathJax using an external Content Delivery Network that is horribly slow. That last scenario is very unlikely but it is the sort of thing that can cause problems.
Can you also confirm your setup, e.g. is it plain MysQL on some kind of Linux with Apache, or have you got SQL Server running on QNX with raspberry PI hardware on a clustered back end running on a distributed OCFS file system (exotic and absurd example there but you get the picture)