Specifically, half size when you factor in all three dimensions.
"Half size" is good choice when you want a character to appear significantly smaller without being "tiny". There's no doubt she's a lot smaller, but she can still do most everyday things.
She won't have to literally climb the sofa to sit on it, for example.
The relative eye levels that naturally result cannot be helped. What am I supposed to do, make Nanase 70% size? Inconceivable.
I don't think Nanase actually thinks in Japanese all the time. Based on what I've heard from bilingual people, it would depend on context, alternate, be a mix, etc.
In the case of the comic, however, I think it could be confusing to mix it up like that.
It presents the question of why I chose a particular language in that moment, be it entire thought bubbles, or individual words.
The sensible thing to do is to not bother with indicating a different language being translated in thoughts unless it is somehow relevant to the story.
But I did indicate that earlier, so for at least this storyline, I'm going to keep doing that with Nanase's thoughts. Stopping now would raise the question of why, and not everyone reads these commentaries, takes notes, and commits them to memory. Might as well stay consistent with it.
Additional Ramblings on Translating Thoughts
One reason I think "this is a translation" indicators for thoughts are unnecessary is that even thoughts in the language the reader is reading are likely being translated.
Plenty of our thoughts aren't neatly organized, or even put into words, for convenient comprehension by others.
"I want a sandwich" could well be a translation of someone recalling an olfactory memory and feeling hungry. Those words might never have echoed longingly in their mind.
Granted, they might have.
They do want a sandwich.