The meanings are different. At Google Books:
"One thing I found it hard to"
About 31 results
Sing, Whisper, Shout, Pray!: Feminist Visions for a Just World-
Page 570 M. Jacqui Alexander - 2003 - Snippet view - More editions
But one thing I found it hard to be generous about was that
Cornelia's mother never offered me anything to eat
This is where the whole situation that requires quite a description
"the whole situation about Cornelia's mother never offering her anything to eat"
was difficult to cope with.
On the other side, without "it":
"One thing I found hard to"
About 63 results
Octavius Mint and the Indigo Dragon: The adventures of an ...
William Stafford - 2013 - Preview - More editions
This idea was one thing I found hard to swallow.
Here the thing/idea itself was hard to swallow.
OK, prompted by a question from Peter Schor (thank you, Peter), I've continued my research.
The main point is that "find" is a transitive verb and it must be provided with a clear/recognizable direct object.
The "one thing" in front of the verb is confusing the situation, as it can be taken to be that direct object.
Let's separate the antecedents from the verb, by using an "and." Now at Google Books we find:
"and find it hard to understand"
About 4,360 results
"and find hard to understand"
About 84 results
We can conclude here that an long infinitive such as "to understand" is not seen by "find" as a clear-enough direct object, and that "it" becomes necessary, which I believe is coded in some grammar books/rules.
Now, what happens when "one/the thing" pops in right in front of "I found," thus in the proximity of the verb?
Well, as shown by the examples in the above, if what follows "hard" is a clear short infinitive phrase such as "to swallow" "one thing" is taken as the verbal object, and the need for "it" disappears. Other examples:
"One thing I found hard to believe"
"the one thing I found hard to give up—the ocean"
However, if what follows "hard" is a complicated infinitive phrase such as "to be generous about Cornelia's mother never offered me anything to eat", it seems that the native speakers feel the need to switch the focus after "find," "one thing" becomes negligible as a direct object and "it" becomes necessary.
I believe this is a matter of subjective judgement, which the native speakers perform on the fly — thus the variation.
This is the best I could come up with for now.