You’ve just discovered that you have an inadequate hosting plan.
Shared hosting requires that resources be shared fairly between the websites hosted on the server. This is done by many means, limiting disk storage space, limiting database storage size (intensely hilarious things happen to Magento when it exceeds this), throttling cpu use, limiting number of inodes down to some arbitrary low limit, limiting file storage. Planning to use these type services with Magento is a plan to commit business suicide.
If this is a supposed VPS, they’re limiting the number of files because they’re attempting to run too many virtual machines on the same host.
In your plan, disk space is cheap, so they give you the moon but put an arbitrary limit on number of files. You can waste loads of time doing arbitrary stuff to live within arbitrary rules or you can vote with your dollars and leave. Ecommerce is too important to have your site crashing every time you turn around due to such jackassery as this.
You move to a hosting provider that understands Magento’s needs and provides the resources and optimization for it to run as well as disk space for your content.
Magento will run as fast as and as reliably as the resources you are willing to pay for. You don’t necessarily have to pay more, but you need to pay someone who cares.