How it used to work was that the notification line didn't show up at all unless you had notifications, right? So any notification added a whole bolded line to that welcome box and caught your attention right away. There needs to be something equally distinctive to catch your eye up there.
I think the most recent themes Garchompin'/Yggdrasil could do it really easily. The background of the notifications bubble could change to a bright colour, or even fade/flash colour, whenever the number inside is not zero. I wish that design could be implemented with other themes but it wouldn't work in themes with a heavy basis in the default vBulletin. The text needs to be fairly big to balance out the design and that's not usually the case with the default placement of the notifications. (If they all had a top bar like that, maybe it could be done though!)
What twitter has done recently is give you a little pop-up in the bottom-right corner of your screen (just on that page) when you get a notification. I believe it goes away very soon after, sooner if you hover over it and off with your cursor. You could look into doing something like that? It's a little invasive and honestly, kind of annoying, but people might prefer it over accidentally ignoring their notifications for hours on end. :(
Alternatively, you could just go back to what we had before and add a line in when there are notifications. Even if it's just a bolded "You have notifications!" right above the notification line, it would be a visual change that people might pick up on like they did the old notification system. Honestly though, the welcome messages should be drawing attention up there whether there are notifications or not. But for me, within an evening, I'd already retrained myself to just not look up there if I noticed anything slightly amiss because it was only ever a change in the welcome message and I was already starting to get repeats. So just one line might not cut it anymore. (But it'd probably work for me since I turned the welcome messages off, haha.)
I've been having a lot of problems noticing when I have notifications now. I was starting to type this up when I went "I wish I had a notification to test out how it might look on other themes..." and lo and behold I had two, lmao.