As mentioned, full specs will be helpful.
An HDD or a Case/Cabinet serve fundamentality different purposes (akin to fuel or food? Both important, but context is needed. If you're starving.... then there;'s an obvious answer)
Some aspect of dust is to be expected., but if you have a cheap case with a lot of holes for ventilation (and happen to live in a dusty environment), a new case might be a good idea - but if you're dealing with a failing HDD (or just a slow 5400rpm), an upgrade there would likely be beneficial.
The TPM header is only important if you wish to use a TPM Module. For 99% of users no, it's not important.