If you know there’s a covops ship in your system you should be far more careful.
As you noticed they don’t need to scan your site if they already bookmarked it.
In fact if I see other players in local while exploring and I cannot tell what they are flying on dscan I do a check on zkillboard to see what kind of things they do.
And if one of them flies Asteros or other cloaky ships, or worse, has explorer kills, don’t hack in that system if you don’t want to take the risk.
Asteros do have the usual targeting delay aftr decloaking though so I once thought it was a fun idea to hack a site in a system with a neutral who I knew was likely flying an Astero.
Second can he decloaks on me, but as I was prepared I immediately warped off before he could scram me 5 seconds after decloaking.
But with a Raptor buddy he could have done that with much less of a delay.
TL;DR: do not hack when you know covert ships are likely hunting you in that system.