Hey gioblack, welcome to the forums! I hope you've had a good time with ACIII Remastered
For the shop not being marked as explored, this is a purely visual bug - it shouldn't affect any gameplay, including trophies or achievements. Sorry for the confusion.
Regarding the deliveries, the percentage increases per region. For example, doing one delivery in New York doesn't change the percentage, but doing all three in New York boosts it to 33%. So, please make sure you've done all of them in each region, perhaps by checking a guide.
Let me know if this clears things up, or if I can further explain anything!