I have to agree that Malware hides there most often. However, I guess you're fine to have that checked and then, if you suspect malware, uncheck it. Strangely (and I maybe wrong) I think it looks at creation date not modification date.
So, the "Only delete files in Windows Temp Folder older than 24 hours" is in place for the instances that Windows will delete a file even if its in use.
The box is there for the times you need to empty the folder for what ever reason.
I'm going to leave the box checked just in case a program is using a file.