JSP knowns nothing about HTML at all. Nor JavaScript. Nor CSS.
All the HTML, JavaScript and CSS markup in a JSP template is just template text and is not processed or parsed in any way by the JSP engine. It could be Swahili for all the JSP translator cares. So whether the template text contains HTML5, or HTML4, or random keystrokes caused by an iguana walking over the keyboard doesn't matter one iota.
So no, whatever your problem is, it isn't the use of HTML5. The problem lies elsewhere.
Please read
this article for more info on how JSP works.
Describe the problems you are having, and post the relevant code sections (be sure to UseCodeTags).