First, a little philological note: hoi polloi οἵ πολλοί literally translates as "the many" and is often used in a derisive sense. Aristoi ἄριστοι literally translates as "the best," but is often used as a marker for the elite or the select. Hence, for example, the English word "aristocracy." That this division is common in Greek philosophy is beyond dispute, but what it means, i.e., who counts as "the best" versus "the many" is an issue that can change, and, at times, those referred to as aristoi are a bit closer to what, in contemporary English, we might call a meritocracy, i.e., those who are the best at ...
Second, Heraclitus is exceptionally hard to interpret, not only because so few of his writings/sayings (around 135 fragments of various lengths but usually no longer than a few sentences, not collected in a single book, but rather quoted---often from memory---by a wide variety of authors), but even in antiquity, his work was known for its obscurity and he was nicknamed "the obscure" and "the riddler." Furthermore, some of the earliest commentators we have on his work (Plato and Aristotle in particular) had little interest in offering a "correct" interpretation---Plato often refers to him derisively and it is questionable whether Aristotle had ever read the book he is supposed to have written.
What is clear, however, is that he long had a reputation as someone who saw himself as superior to other men. Thus, the ancient biographer, Diogenes Laertius (separated by at least 800 years from Heraclitus) records that
He grew up to be exceptionally haughty and supercilious ... Finally he became a misanthrope, withdrew from the world, and lived in the mountains feeding on grasses and plants.
Kirk & Raven, The Presocratic Philosophers, p. 182
That said, he does, at times, appear to have written things that were almost democratic in spirit:
It belongs to all men [anthropoi] to know themselves and to think well.
Thinking [phroneein] is shared by all.
DK 116 & 113
The first, as Kahn points out in his excellent commentary, The Art and Thought of Heraclitus, offers a democratisation of the Delphic oracle's famous injunction gnothi seauton, "know thyself," which suggests something that is hard to do, something that only few can achieve. Yet, Heraclitus seems to be saying that, however hard it may be, it is something incumbent on everyone, and hence something everyone is capable of.
Yet, despite this sense of capacity, it is clear that Heraclitus has a sense that very few fulfil this capacity, thus, for example:
One man is ten thousand, if he is the best [aristos].
The best [aristoi] choose one thing in exchange for all, everflowing fame among mortals; but most men [hoi polloi] have sated themselves like cattle.
What wit or understanding do they have? They believe the poets of the people and take the mob as their teacher, not knowing that "the many [hoi polloi] are worthless", good men [agathoi] are few.
DK 49, 29 & 104
So what are we to make of this? Obviously it is open to many possible interpretations and not much will be done to resolve this. Perhaps the most charitable reading would be to say that for Heraclitus, everyone has a certain equality, but that the majority do not choose to exercise that equality, that equal capacity, and so those that do, those that truly excel, should be set apart and held up as paradigms.
Finally, on Popper, although the interpretation that totalitarianism may grow out of Heraclitus' thought is not in and of itself wrong, it is possible that Popper had additional reasons for offering a less charitable reading of Heraclitus: he is cited, by Engels in Anti-Dühring as a fore-runner of historical materialism.
Bibliographic note: My citations of the fragments are given by their Diels-Kranz number for easy reference, e.g., in this resource. The translations are from Kahn's The Art and Thought of Heraclitus, though I have added the transliterated Greek words where I thought relevant to the question.