Since you employee SharePoint and better user of SharePoint functionality, store them in SiteAssets library, try to avoid layouts folder, even u can keep caching bundling the files and if you engage MDS, SharePoint take care of many of things for the performance is considered
I recommend to place it in site assets library.
You can make use of default MDS, Caching, bundling, performance, access related and dynamically change at any point of time as per customer requirements with out any deployment or down time(very important for customer related point of view)