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Yes, but if you use 1M for stack you havr less ram for you code, and I'm always in short of it in my game ports.
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Try tracing the free memory. If the emulated floppy try to allocate 1.44M of space, probably you are consuming all the RAM left. Chech if malloc returns NULL too. Some program can omitt this assuming to run with system with a lot of phisical ram (and maybe vram)
C64 floppys are only 170k
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The stack size is defined weak. So you can override it in your source and set it to a larger value - say 1MB.
u32 __stacksize__ = 1* 1024 * 1024;
https://github.com/smealum/ctrulib/blob/master/libctru/source/system/stack_adjust.s
Where abouts would I have to do this exactly?