As the title says, adding in ways to add nanopods via in game achievements would make the game less freemium.
For example, "Make 5 modern houses/duplexes" awarding 5-10 nanos would be a meaningful way for players to progress in important areas of the game. Another example could be "activate all resource nodes" or "get all resource nodes to level 5"
For larger achievements, such as getting a unit to max rank, nanopods could be awarded depending on the difficulty of ranking that unit. This could also give a good incentive for collectors/completionists.
Overall, this gives the game a more quest like feeling that makes players focus on important progression that remains intuitive through game design and has genuine, meaningful payout. It also rewards those who stick with this game by giving them nanopods and eventually being able to get the units they want (basically, longer play time = naturally more achievements = more nanos). Finally, this also allows player to spends nanos for units they think are COOL (ex: ninja is cool af but no one actually gets it because of the cost) without feeling nearly as guilty.