Potters captain Shawcross is set to be absent for the next few games due to a back injury that forced him off in the first half of last Saturday's 3-1 Barclays Premier League victory over QPR.
It was announced two days later that fellow centre-back Huth had left Stoke to join Leicester on loan for the rest of the season. But Hughes says the deal had been "completed" the previous Friday and that it was too late for it to be halted by the time Shawcross sustained his problem.
The manager - who is set to pair Marc Muniesa with Philipp Wollscheid at the heart of his defence for Sunday's top-flight away clash with Newcastle - said of the Huth switch at his pre-match press conference: "It was too far down the line.
"It had been completed on the Friday prior to the game, and you can't legislate for those things - that is what happens.
"Hindsight is a wonderful thing and if we had (known Shawcross would get injured) we probably would have stepped back, away from allowing Robert to go.
"But things had moved on, everything was in place and it had been signed off. There wasn't any room to manoeuvre on that."
Huth would not have been eligible to play against Newcastle on Sunday anyway as he still has one game left to serve of the two-match suspension he was handed by the Football Association after breaching rules relating to social media comments.
But he may have seen some action for Stoke soon after, with Shawcross - who it had initially been suggested was affected by a groin issue - looking set for at least a couple of weeks on the sidelines with an injury Hughes has confirmed relates to the 27-year-old's back.
"He is a little bit sore at the moment," Hughes said.
"He has an issue with a disc in his back, which is a little bit inflamed. That is causing him a problem and we are trying to get it to settle down somewhat, which is ongoing.
"We think he is likely to be out for a couple more weeks if everything goes to plan and that is a shame, because he has been playing exceptionally well."
Hughes has stressed he regards Muniesa as "good cover" alongside Wollscheid, and that he is "quite comfortable" overall with the strength of a Stoke squad that was only added to in the winter transfer window by the latter's arrival on loan from Bayer Leverkusen for the remainder of the campaign.
The Potters tried before Monday's deadline passed to bring in Tottenham's Aaron Lennon, who instead opted to join Everton on loan. The Staffordshire outfit were told the winger felt he had a better chance of getting first-team football with the Merseyside outfit.
Hughes says he had "a couple of targets" that did not materialise into completed deals, but has also emphasised there is a greater focus on making the most of this summer's window.
Asked if he had been biding his time until summer, Hughes said: "Yes, there is a little bit of that in our thinking.
"It is difficult to get the quality you are really looking for (in the winter window).
"You can put things in place and have conversations that maybe are put to one side and you revisit in the summer when there is less time constraint on your dealings, which can help.
"We have got resources to go into the market, but we'll do it when we think we've got a real opportunity to get the ones we really want - and if it means we have to wait a little bit longer, then so be it."