Many times I have these email threads in the message list that occupy more than one row. Meaning, I reply to an email, it stays in conversation, but when the other person replies, I receive a new email in another row/thread. I don't understand why eM Client doesn't keep them all in one conversation. It doesn't happen to all emails, but it does to some like ticket replies, etc., even though the subject remains the same (important to note).

So, I've been trying to find a feature that lets me search to find the same email so that I can organize them (whether to read past replies or to delete them), without having to manually type/paste the subject in the search bar.

I am thinking that you can add a context menu called "Search Similar" or "Find Similar" or "Find Related" to an email message. When clicked, it would show all the similar ones with similar subjects, perhaps even it would search/filter by the same sender as the one I'm right clicking, just to make sure we don't get random search results.
It would then display all of those as if I searched for them.
It would be of great help so that I can easily find all those emails.

Or, do like Outlook.com (see below) and let it be a parent menu with 2 submenus so that we can search/find either by sender or by messages similar to this conversation.

Gmail has a "Find emails from x" recipient.
Outlook.com has the best one: "Find related". You get 2 options: Messages in this conversation. Messages from this sender.

Hopefully you can implement something similar to Outlook.com

Note that the History view on the right sidebar doesn't help much. It just shows all replies, doesn't matter in which email thread, and is a convoluted view which I can't see myself using for this case. It helps a bit in other cases.