The difference is that the smartcard chip manufacturer NXP produces smartcard chips. NXP's most known smartcard chips are SmartMX (P5C*) and SmartMX2 (P40C*, P60D*). Besides these, NXP also produces some not-so-smart smartcard chips (e.g. MIFARE DESFire MF3ICD*).
JCOP on the other hand is the name of a Java Card compliant and Global Platform compliant operating system. JCOP was initially developed by IBM and is now maintained by NXP. JCOP is only one option for an operating system that can be used on NXP's smartcard chips (note that the "not-so-smart" smartcard chips don't use such a complex operating system). J* is the version number of the JCOP platform (yes, there are many of them).
So why do smartcard vendors avertise their product by operating system name & version while NXP avertises their products by chip name?
Simply because that's what each of them sells:
- NXP mainly sells chips. NXP's customers decide what operating system they want to have (many of the SmartMX* datasheets list some of the supported systems as product options).
- Smartcard manufacturers sell smartcards that have a certain configuration. In terms of Java Card products that's typically the type of operating system and the supported Java Card version. After all, one of the main ideas of Java Card is that it abstracts programming from the actual smartcard hardware.
Note: with many parts of this answer NXP and their product names can be replaced by "arbitrary smartcard chip manufaturer X" and their respective products.
UPDATE:
- If you buy a smartcard (you typically don't easily get chips without the card) from a smartcard vendor, you buy one that contains a specific OS (that's why the vendor will advertise it with a a specific OS name + version).
- If you happen to be a smartcard manufacturer/direct integrator of smartcard chips and buy them directly from NXP, you will choose the OS that the chips will contain when they are delivered to you.
- The OS is typically "installed" during production time (ROM mask) so you can't install/modify it after the production process.
- The best overview of JCOP versions I found so far is in this document. Though it does not contain the latest versions.