Hi,
First, I don't think it comes from your update of HikaShop.
So you're saying that the order status of paid orders is still changed automatically by the payment plugin. Can you confirm this ?
Because normally, when a payment plugin automatically confirms an order, it fills the "reason" of the history with "automatic payment notification received".
Based on your screenshots, it seems this was the case before and not the case anymore.
And if the plugin is not automatically confirming the orders, it's normal that HikaShop doesn't send the emails.
And in that case, the problem has to be in the payment plugin.
Supposing that the plugin is still confirming the orders automatically, it's the plugin which tells HikaShop to send the emails. So again, an update wouldn't change anything to this.
Another potential reason would be that you updated your PHP while you still have old overrides in your emails which crash when HikaShop tries to generate the emails. This could lead to the order status being changed without the history being properly updated and the email sent. An easy to check if this is the problem is to go in the System>Emails menu and to try the preview the different emails that you're not receiving anymore.
If the preview fails, then you should see an error message explaining where the problem is in your email override. Once the preview is generating properly, it should then work normally again.
Also, I would recommend checking the PHP error log of your hosting. You might get interesting fatal error logs from there pointing at the problem.