The Premier League bowed to pressure to abandon the handshake ritual on Thursday night, ahead of this weekend's west London derby at Stamford Bridge to avoid any chance of it affecting Blues captain John Terry's upcoming racism trial.
Sunday's match will be Rangers defender Anton Ferdinand's first trip to the home of his side's arch-rivals since October's reverse fixture, after which allegations emerged he had been racially abused by Terry, something Terry categorically denies.
QPR boss Hughes admitted he was surprised at the league's suggestion his players applaud their counterparts onto the pitch before the match kicked off.
He said: "They were looking for solutions for the game at the weekend and the Premier League were throwing things out there and said at one point that one alternative would be to form a guard of honour and clap Chelsea onto the pitch, and I'm thinking there is absolutely no chance of that happening.
"But that is where we were getting to, there were discussions going on, that was the one that pricked my ears up. That is the only one I was told, so there you go."
The Premier League later denied the suggestion had been made, with a Premier League spokesman saying: "It was never under consideration. The board would never have suggested or agreed to it."
Hughes believes the league should look at whether the handshake ritual should exist at all going forward.
"It needs to be on the agenda," he said.
"The Premier League need to clarify their position on it and make sure it is there for the right reasons. I said that last time you have to understand the thinking behind it - it is all very credible and a good idea to have that put forward but the reality of it means it can sometimes be compromised.
"Unfortunately, it is becoming a negative and, if it continues to be, it has to be stopped. I think sometimes it is an irritation - I don't think there is any real desire to do it."
Ferdinand insisted none of the players would be affected by the decision to scrap the handshakes and that any abuse he received from the Chelsea support would not impact on his performance.
He told the Evening Standard: "My view is whether you shake hands with a player before or after the game doesn't really matter to me. It is about playing football.
"My team-mates have said nothing to me about it because we are just treating it as a normal game. It is not about me or the current situation - it is about QPR and staying in the division.
"It is not for me to talk endlessly about handshakes - what matters is what happens in the course of 90 minutes.
"The Chelsea fans believe what they want to believe. They have their own view on what's gone on, and if they are going to give me stick, that's their problem.
"All I can say is that it won't upset my game. If they think that's what's going to happen then they have got another thing coming."
The Football Association cancelled the usual pre-match handshakes before January's fourth-round cup tie and the Premier League have now followed suit, a decision Chelsea's interim manager Roberto Di Matteo said he "respected".
But he was in favour of the ritual in principle, adding: "To show respect to your opposition is a good thing, so I'm not generally against it."
Di Matteo revealed he would remind his players of their responsibilities ahead of a derby that was dogged by controversy in October's reverse fixture.
He said: "I always speak to my players. They will be focused on Sunday to try to win the game. The rest is for other people to worry about.
"We have to channel our energies to win the football match - that's all."
Di Matteo had no concerns about the state of mind of Terry, who was sent off in Chelsea's Champions League semi-final triumph in Barcelona, ruling him out of the final.
"I don't think that's going to influence him," Di Matteo said of his skipper.
"He's got a few years under his belt now and has dealt with setbacks before. He'll be very good."