Look, I might come across as a stickler here. Ultimately, do whatever you want. Experiment. Life's short. Japanese is lots of fun. And your comic could look really cool with mixed sfxs! But if you want my opinion: it doesn't matter where you are, but how well you understand the language to avoid making bad mistakes.
How bad is it to make mistakes? That depends on what kind of comic you're making. Is it a just-for-fun or practice comic, who cares. But if you want to print it at some point or distribute it more widely, you might not want to become known as the dude with weird or wrong Japanese words thrown in. (;
So if I were to make a little checklist: 1. can you actually read what you're writing, 2. do you understand the cultural context of what you're writing, and 3. do you understand the grammatical structure?
The first point is self-explanatory. Are you just throwing in the cool-looking ザーザー that you often see in rainy scenes? Or can you read it?
The second point: (Just as an example, this isn't a big deal if you get it wrong, it's just what popped into my head) Did you just do a quick google search and find out that it was an onomatopoeia for rain, or do you know that there are dozens of different ones for different kinds of rain, which could be more appropriate for the scene you're showing? (My personal favorite is potsu-potsu for light dripping rain.) Rain specifically, due to the long rainy seasons, has had quite a strong impact on Japanese culture, which is expressed in both language and arts.
Or are you unintentionally using stereotypes, such as, dunno, everyone saying "waa~" all the time without knowing that most people actually don't use it that much? (Except girls/women wanting to look cute I guess - but I rarely heard it used much.)
The third point: This is also pretty obvious, but Japanese grammar isn't based on the same foundation as English. The sentence structure and use of words is different. This might make you feel compelled to directly translate from your native language to Japanese - and in most cases, that won't work.
But hey, if all you want to do is to make your comic look even cooler in some places, I'm sure it'll suffice for you to look up what's being used in Japanese comics, double- and triple-check translation and context, and put it in. You could ask on this forum too, there are a bunch of people here who know enough Japanese to help if you're unsure. Just... Don't use shonen or moe shows as a point of reference for how people actually speak. xD
Oh! And! Some people have mentioned alienating readers. I'll be perfectly honest with you: I don't read the sfx or onomatopoeia. And I'm sure there are plenty of readers who skip over them too. If I see a sword dramatically slicing the air, my brain adds the sound on its own. . Furthermore, manga has become so wildly popular in so many countries with the original sfxs left in, so I wouldn't worry too much about alienating readers. Chances are that your comic will be the most appealing to that audience anyway.
(So why do I care so much that I wrote a longass post? Because I'm a language nerd. And perhaps because I'm a bit sick of people rushing to conclusions about other languages. Like German is misused and misunderstood a lot... "Jawohl!" is not an everyday "yes". "Führen" or "Lokführer" are not bad Nazi words. Etc etc. Also I'm incapable of writing short posts.)