The Potters completed the signing of former New England Revolution striker Agudelo on a free transfer in January, despite being denied a work permit for him in November.
The 21-year-old was immediately sent to Dutch side FC Utrecht on loan while Stoke prepared a second application, but the Barclays Premier League outfit announced on Saturday they had been unsuccessful the second time around as well.
Hughes now thinks that is "probably the end of it" and has suggested the club will not be trying to make any other non-EU signings any time soon.
The Stoke manager, quoted by The Sentinel, said: "We are desperately disappointed for the boy himself because he's made a big effort.
"He came to us and then went out to Holland because he wanted to do everything in his power to help himself.
"Unfortunately, that's probably the end of it.
"You never say never, but we would probably have to wait something like two years for him to play the required number of games.
"I just think that given what seems to be happening, it's very unlikely Stoke City will be going to any work permit hearings in the near future.
"There would be no point, given the attitude to bringing in non-EU players if they are not £20million to £25million players because it's very unlikely we would get them in.
"For full internationals with great potential, there is no pathway."
Source : PA
Source: PA