Analyzing it from a psychological standpoint...
UboaaaaAAAAAAAAAAAAAAAAAAAAAAA~~~
I think the event of Uboa's appearance manifests the fear of change and of what is known in Troperville as "Schrodinger's Butterfly". (Yes. BUTTERFLY. No cat here, sorry.)
The fear that something seemingly nice and normal(-ish -How close does ANYTHING in YN ever come to normal?**) can change with a teeny-weeny seemingly inconsequential act, like flipping a lightswitch.
KITTY SAYS: "Or people are just creeped out by suddenly-appearing pixel monsters."
Because we can't always foresee what the consequences of our actions will be, the thought that something that has become routine (like walking in and out of a room a hundred bajillion times to flip a fucking lightswitch) can bring on a change we may or may not expect, one that we know will eventually happen in the back of our mind (because, let's face it, YN is an obscure game even in Japan! Half or more of the people who play it only heard of it because of Uboa's memetic mutation) yet we think the disaster will be stalled for one more time, the thrill of knowing it's always there and possible, is terrifying.
-And then, even when we expect that change, we don't necessarily want to accept it, making the realization all the more frightening.
Also, I agree almost wholeheartedly with the below Anon in his/her interpretation of Poniko's Barbie paradise.
**Well, besides the obvious Toriningen, which, depending on your vantage point [THIS troper finds them completely realistic for sure- high shool girls are SCARY] can be seen in varying degrees of believability, but again, "Your Mileage May Vary".