On top of that, HYDRA's historical involvement in SHIELD is somewhat of an open secret. SHIELD recruited HYDRA scientists like Zola in the post WW2 time period for their expertise. Any references to them would be brushed off as obvious, though possibily politically inconvenient.
What WASN'T known was the hidden agenda of this group or the extent to which they continued to recruit
And proliferate. And that's not something that's just going to be Laying around in a password protected file.
Even fury couldn't get access to the information he suspected was there, which is why he staged a hijacking to have Widow steal it. And even then that data was protected by a self aware AI program that shifted encryption on the fly, designed by Zola himself to keep peoples hands off of it.
Expecting Tony to hack random low level shield computers is one thing, expecting him to try to break into HYDRAs inner circle and out hack Zola (who he doesn't know exists) is a completely different issue.
Give it up, that's not a plot hole.