These are very good questions. In the first question, the answer is yes, even if hello packets are being recieved from a router, the SIA state will still kill the neighbour adjacency. You can think of the Stuck in Active condition as an additional condition for which neighbour adjacencies are killed.
As for your second question, yes you’re right, the SIA reply may also fail to reach Router 1 due to congestion. Only one SIA Query is sent at 90 seconds. However, the purpose of the SIA Query and Reply feature is not only to resolve eigrp failures due to congestion, but also due to the waiting time it takes to allow additional routers to respond to queries. Let’s say you have six routers in this configuration:
R1 loses a router via the interface to the left. It sends a query to R2, which sends a query to R3 and so on. At 90 seconds, R1 sends is SIA query to R2. R2 WILL ANSWER with an SIA reply EVEN IF it doesn’t yet have an answer to give R1, because R2 is also waiting on the other routers to get an answer. This saves the relationship and the rebuilding of the routing table. The timer then goes back to 0 and after another 90 seconds the query goes again.
I hope this has been helpful.