Is there any particular reason why the noun おなか goes with verb すく while the noun はら goes with the verb へる? Would it be weird if I use おなかへった or はらすいた?
While on the same topic, does the 'starving' onomatopoeia ペコペコ go with both おなか and はら?
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Besides the phrases being idiomatic (fixed), there is a slight difference in the meaning of these words.
お腹 (onaka) means stomach, although it can also mean belly 腹 (hara) means belly
You can also tell this from the fact that the pronunciation for
お腹 (onaka) is related to
中 (naka) 'inside', which implicates stomach. Therefore, even with the same predicate, they mean different things:
お腹が痛い 'my stomach hurts' means stomach ache caused by eating too much or poisoned food 腹が痛い 'my belly hurts' means laughing to death, (in addition to the meaning above)
In the case in the question,
空く 'become empty' goes well with stomach rather than belly.
へる 'lose volume' goes well with belly rather than with stomach (stomach is just a wall).
I don't know who told you that each only went with one, but I don't think that's true.
I have most definitely heard お腹【おなか】used with both verbs. And Google seems to agree (100ks hits for either).
腹【はら】is less common in any case, and 腹空いた【はらすいた】 sounds a little unusual, but Google still gives over 60k results for it, so I doubt it could be considered 'rare'.
ペコペコ describes your feeling of hunger (among other things), not the particular emptiness of your stomach/belly, so no reason to use it with either word.