Based on what we know, there's no reason to assume Jango knew (or cared to know) any details about the clones' enhancements and programming, let alone the most closely guarded secret of the project. They kept him around as a living genetic donner for whenever they needed more material; that seems about the extent of his involvement in the endeavour.
To date, the only people we know were even aware of Order 66 are Palpatine, Dooku, and some senior Kaminoans such as Lama Su & Nala Se. So it appears to have been strictly need-to-know; Maul said even he wasn't privy to the details of the plan, and was just as surprised as the Jedi were when the clones turned.
Indeed; from conversations with Tyranus in the episode ('Conspiricy') it's debatable how much even the Kaminoans actually understood the purpose for which Order 66 was actually intended. Only that it's existence should under no circumstances be revealed to the Jedi.
The very fact that they only knew him as Tyranus and not Dooku seems to support this idea. The details and exact timing of events remain somewhat obscured, but Dooku did claim that Sifo-Dias worked with him to commission the army. We also know from 'Tales of the Jedi' that the plan was already in motion with Dooku's direct involvement before he formally took the name Tyranus, so how the Kaminoans came to know him by that name isn't clear, though one might suppose he just showed up using that name, and somehow convinced the Kaminoans that he was Sifo-Dias' designated representative or proxy. Then proceeded to go recruit Jango as the template.
For his part, Jango only seemed to be motivated by self enrichment (he was paid a LOT of money) and the promise of a legacy in the form of Boba.