Thanks. 1000 Downloads in 24 categories is not really a lot. So this cannot be the reason.
When I test your website all pages (also pages with much Download links) are loaded very fast. So I see not really a problem.
My server provider inform that "Checking on this for you I can see that one or more of your sites is consuming more MySQL resources that it's allowed.". The sited example queries all related to jdownloads, Please help me to rectify error. My jdownloads version is 3.9.8.6
That is logical and normal. Check self your start page, the most content will be created from the jDownkloads extensions here (component, module and plugins).
By the way, has your hoster tell you anything about his mysql limit values?