I don't think it will have an effect. It just shows the crowd's displeasure at Moyes substitution decision making.
The decision at Bolton was booed because we were searching for a winner, and it appeared Heitinga for Jelavic was a defensive substitution that would have ensured we got a replay. Thankfully Heitinga scored, but if he hadn't, EVERY Evertonian would have been bemoaning a 'defensive substitution' (even though in reality it did allow Fellaini to push forward).
Today, we were 3-1 down at home to a **** second from bottom team, desperately seeking a goal, and Mirallas had been one of the few having a good game. When you think about it logically, he's coming back from injury and may not be able to play 90 minutes yet, and we need to take care of him. But at the time, in the heat of the moment and amidst much frustration, a striker for a striker substitution seemed rather cautious. Fans wanted to see Mirallas alongside Jelavic & Anichebe.
There are reasons for the booing. It's not mindless stuff, it's passionate fans voicing their opinions. I'm sure Moyes has a thick enough skin by now after 15 years as a manager to cope with it. It's heat of the moment stuff, it's not a sustained hate campaign. Everyone knows Moyes, generally speaking, is doing a good job. Just that some of his decisions (persistence with Heitinga, Jags at right back, etc) are very divisive and unpopular with some.
In short, people don't boo and overly scrutinise substitutions when the team is winning.