Thanks for all the comments and suggestions, and this is what I believe happened.
The wallet was sent P2p, and not from a recognised supplier. I suspect this raised a red flag, and customs decided to investigate. The local depot didn't have the resources for this, so they sent it away for analysis. The bankers virus probably slowed down this process, which is why it ended up taking 4 months to deliver. I understand that it is easy to send Bitcoin via the blockchain, but this leaves a permanent record. Using a loaded wallet for a money transfer is closer to a cash payment, and doesn't leave any record of the transaction.
Interesting, that's the most probable scenario that happened in the customs. But, it would be nice for them to repack things up since they haven't found anything critically suspicious on the package. Though it raises a red flag, but It's sure have undergone meticulous process before you recieved the package right?
Maybe wallets with viewable balances, but secure withdrawals will become the cash of the future.
I haven't tried using hardware wallet as well, but base on this story, I have just learned that such scenario is very possible to happen not only for you, but for anyone else in the future including me. So, I agree with this initiative.