not sure about a best practice, but for the Object portion at least I essentially follow the SDF XML Reference (/app/help/helpcenter.nl?fid=SDFxml.html) for directory names and then logically group to follow NetSuite site center tab/category structure
dbarnett
01/20/2020, 7:56 PM
ex.
Objects > Lists, Records, Fields > Fields > (entitycustomfield, itemcustomfield, transactionbodycustomfield, etc.)
Objects > Scripts > (clientscript, suitelet, etc.)
always open to suggestions for other/better practices though :)