A "clone" would be a car that started out as a Malibu (or other), that a previous owner added the SS emblems, etc... A clone is a car that was not "born" as an SS... Clones can be built to various degrees of accuracy, from a few "SS" emblems to a car with all the required SS items, including a complete "date correct" replacement engine... Some cars might even have "cloned" documents... Often clones fall somewhere inbetween, often "looking" just like the real thing, but having a completely different engine...
In general, clones are worth less than a "non-matching numbers" car (assuming the cars are identical)... For some reason, the original "SS" heritage adds value (I can understand if the car is all original, where an SS is worth more, but once its been modified/etc, its only a sum of the parts, and they can be the same parts).
For 1969 and up, there really is no way to tell a "good" clone (with the correct pieces) from a "real" SS, without paperwork... 1964-1968 Chevelles (and 1972 454 powered cars), the VIN numbers indicate if the car was an SS from the factory, or not...
Could you tell about your car? No... The 69 SS really only differed from the 69 Malibu with some bolt-on items, most of which were optional on either model anyway... The 396 was limited to the SS option, but most other pieces were available for Malibu's too (buckets, disc brakes, guages, 12-bolts)...