By modern standards, yes, writing a bullet hell shooter game is not hard.
But ZUN started on the PC-98.
To put that platform in a western context, imagine if IBM had gone with planar graphics for VGA. Or an Amiga with no coprocessors, sprites, or scrolling[0]. You have a lot of pixels to fill and no help to do it with. It can't even run DooM[1]. Most other developers threw their hands up and shipped RPGs, erotic visual novels, or porn. Getting a fast action game running on PC-98 is a genuine accomplishment.
[0] I am aware that I just described a compact Macintosh.
What you described is even better: an Atari ST :)