Libraries like Vue and SEO

How do you tackle sites that should be SEO optimized but also want to benefit from Javascript opportunities like Vue. I'm not aware how much it breaks a good SEO, but I can imagine it's not great. Should I completely avoid it and use VanillaJS or is it okay that some elements are not as optimized, maybe they are just "ignored"? Or can I actually make it SEO friendly?

The problem is that things are build up from components so without Javascript there might be tags like <search></search>, but after Javascript applied it could be (simplified example) <input type="text" name="search">. I don't know if search engines see the Javascript compiled version or they see me as bad for having irrigular HTML.