Isildur probably had a fairly good idea of who had the Three through perfectly mundane means, even if the Elves did not let it out to him and Elendil, which they may have.
Your quote already tells us that Isildur couldn't use the One Ring for its intended purpose, the full quote is:
There was a pause, though the most keen-eyed among the Dŭnedain said that the Orcs were moving inwards, stealthily, step by step. Elendur went to his father, who was standing dark and alone, as if lost in thought. ‘Atarinya,’ he said, ‘what of the power that would cow these foul creatures and command them to obey you? Is it then of no avail?’
‘Alas, it is not, senya. I cannot use it. I dread the pain of touching it. And I have not yet found the strength to bend it to my will. It needs one greater than I now know myself to be. My pride has fallen. It should go to the Keepers of the Three.’
(Unfinished Tales, the Disaster of Gladden Fields)
To the best of our knowledge, Sauron himself couldn't use the relationship of the One with the Three against the Three without actually using the Ring:
But the Elves were not so lightly to be caught. As soon as Sauron set the One Ring upon his finger they were aware of him; and they knew him, and perceived that he would be master of them, and of all that they wrought. [...] But Sauron could not discover them, for they were given into the hands of the Wise, who concealed them and never again used them openly while Sauron kept the Ruling Ring. (Of the Rings of Power and the Third Age, the Silmarillion)
Frodo himself only figured out Galadriel wore one of the Three when she revealed it to him, although some magic was at work, because Sam could not see it. Perhaps this is, in some way, what Tolkien meant when he said they were not used openly.
So bright was it that the figure of the Elven-lady cast a dim shadow on the ground. Its ray glanced upon a ring about her finger; it glittered like polished gold overlaid with silver light, and a white stone in it twinkled as if the Even-star had come down to rest upon her hand. Frodo gazed at the ring with awe; for suddenly it seemed to him that he understood. [...] 'Yet even so, as Ring-bearer and as one that has borne it on finger and seen that which is hidden, your sight is grown keener. You have perceived my thought more clearly than many that are accounted wise. You saw the Eye of him that holds the Seven and the Nine. And did you not see and recognize the ring upon my finger? Did you see my ring?’ she asked turning again to Sam.
‘No, Lady,’ he answered. ‘To tell you the truth, I wondered what you were talking about. (The Lord of the Rings)
Other than this scene, there is no indication Frodo, Sam, or Gollum ever noticed or knew anything about the Three, except after the One Ring was destroyed, and the Rings were worn openly.
On the other hand, it's clearly hinted that many Elves at least figured out who had the Three all on their own:
Of the Three Rings that the Elves had preserved unsullied no open word was ever spoken among the Wise, and few even of the Eldar knew where they were bestowed. [...] Therefore ere the Third Age was ended the Elves perceived that the Ring of Sapphire was with Elrond, in the fair valley of Rivendell, upon whose house the stars of heaven most brightly shone; whereas the Ring of Adamant was in the Land of Lórien where dwelt the Lady Galadriel. A queen she was of the woodland Elves, the wife of Celeborn of Doriath, yet she herself was of the Noldor and remembered the Day before days in Valinor, and she was the mightiest and fairest of all the Elves that remained in Middle-earth. But the Red Ring remained hidden until the end, and none save Elrond and Galadriel and Círdan knew to whom it had been committed. (of the Rings of Power and the Third Age)
(nb: Elsewhere we are told that Saruman figured out Gandalf had one of the Three.)
So did Sauron; he rightly guessed, even if he didn't know:
But he guessed the truth, that the Three had been committed to Elvish guardians: and that must mean to Galadriel and Gil-galad.
(Unfinished Tales, the History of Celeborn and Galadriel)
Though Isildur would likely have been considered one of the Wise in his time, and indirectly informed (since they did not speak of them openly, Isildur would have known that a) the Three were held by the Wise; regardless of who that specifically meant, he would have known it was the Wise among the Elves, which is all we need for that statement to make sense and b) the Keepers of the Three almost certainly would have included Galadriel, the "mightiest and fairest of the Elves that remained in Middle-Earth", and Elrond, who easily qualifies as the second most notable Elf in Middle-Earth, after the death of Gil-Galad. Cirdan also would have been a reasonable guess, though perhaps Isildur would have speculated some Elf-Lord in Elrond's house; it still wouldn't have mattered, though.