correction: tested in lab given answer is right. N,N, Y
1) Inbound rule on subnet1 will deny
2) Inbound rule on subnet2 will deny
3) No rule on VM3 so it would allow connections

Box 1: Yes -
VM3 is Subnet2. NSG2 applies. The default rule will allow communication.

Box 2: No -
VM1 & VM2 is in Subnet1. NSG1 applies. Only traffic on ports 80 and 443 will be allowed. Connection on port 9090 will be denied.
Note: Priority: A number between 100 and 4096. Rules are processed in priority order, with lower numbers processed before higher numbers, because lower numbers have higher priority. Once traffic matches a rule, processing stops. As a result, any rules that exist with lower priorities (higher numbers) that have the same attributes as rules with higher priorities are not processed.

Box 3: No -
VM1 is in Subnet1. NSG1 applies. Only traffic on ports 80 and 443 will be allowed. Connection on port 9090 will be denied.
Reference:
https://docs.microsoft.com/en-us/azure/virtual-network/network-security-groups-overview