It might be hacks. Your best bet to find that out is to disable all hacks and see if that makes a difference.
If you are on shared hosting, it may make an effect, because it's not just your site on the server, but someone else might be using up all teh resources on the server, thus causing your site to be considerably slower. If it doesn't end up being your hacks, you will want to contact your host and ask them to check to see who is using up the resources so they can handle it from there, or upgrade your plan.... or find another host.
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