No way. It means by the end of the business day in most cases. Not midnight.
I've never seen End of Business Day stated on any site's online app. I have seen 11:59 PM EST listed on many sites. You may be thinking of snail-mail requirements, rather than online.
If it state that time, then sure, that time is the deadline. If it doesn't state it, (and some don't), you really need to assume that the close of business day is what is meant. Based on the OP's original question it is clear they didn't state a time or he wouldn't have had the question he did.
If they don't state a specific time, I'm not sure why end of business would be assumed, rather than end of the stated date. AMCAS does not state the time on the app, but buried in the faq is an 11:59 PM EST deadline. Since many schools list thier AMCAS deadline and their secondary deadline with no qualifiers, it would make sense that both mean 11:59 PM EST.
Since it's online, there will be a timestamp for them to see the next morning, if they even get to your secondary the next day (or next week for that matter). I don't think they have someone checking for online submissions until 5pm, and then nothing else counts. If you got it in by 4:59 PM (before end of business), nobody would see it until the next day anyway. That is no different than turning it in at 11:59 PM.
Now, snail mail is a different story. If you're sending LOR's through regular mail, they should arrive Nov. 15 if that is the deadline (except for schools that state "postmarked" by Nov. 15). If you're using virtual evals, then 11:59 PM EST is the latest to send to the school. My premed office assured me of this when they made an error with a letter and it took me weeks to get a new letter from my prof.
OP: In the end, don't trust quibbling SDNers.
😀 It would be best to contact the specific school if you are unsure (which I did when I didn't take my premed office's word for it on LORs). Better yet, submit your secondary online tonight.
🙂 Or give Law2Doc the benefit of the doubt, since his answer will at least make you 7 hours early.