I tested a few games where I kept my starting lineup for the duration of the whole 48 minutes and surpisingly I didn't notice any difference in player performance.
I still won a hefthy number of games and my players performed well up until the last minute, even though some of them had energy as low as 40%.
Even in tight games I'm able to catch up in the 2nd and 4th quarter when the opponent heavily uses their bench, whilst I keep pushing with my starters.
I will run more tests to make sure.

Yes it does. Your players will perform slightly worse as they lose endurance but remember slightly worse may still be better than an opponent. If Lebron were to play 48 minutes its not like in the 4th quarter he would look like some guy from the YMCA.

Also the lower the EN% the higher risk of an injury.

That makes sense, thank you.