No. It's due to hardware limitations. The PS2's Emotion Engine and its eDRAM were capable of generating an incredible amount of particle effects at once--rain, fire, snow, or in this instance, hundreds of bugs. Sometimes the bugs show up, and sometimes they don't. On backwards-compatible PS3s that have the EE chip, the bugs will always show up.
When you're around large amounts of particle effects in MGS3, the framerate drops dramatically because of these hardware limitations (which is probably why they originally kept the game at 30fps). It's also a problem in Zone of the Enders HD, another game with heavy particle effects. Kojima has a reputation of taking whatever hardware's he on at the time and pushing it to the max. On the one hand, it's respectable that he's uncompromising in his vision. On the other hand, his games of the last decade tend to suffer because of it. Then when his games are ported onto different systems, they have trouble keeping up with the PS2's unique architecture, despite it being outdated technology.