The kanji spellings are directly borrowed from China, so it's Chinese that call them so. Cucurbits are originally tropical plants, thus they were all imported to East Asia at some points of history. 西瓜 suggests that it came from Western Regions, and 南瓜 from Southeast Asia. As they are tropical plants, 北瓜 shouldn't exist logically, but according to a Chinese ...
Does the word for squid (ika) come from another language?
Adding on to kimi Tanaka's answer, I see in the 日本国語大辞典 entry here that the word ika appeared in the 播【はり】磨【ま】風【ふ】土【ど】記【き】 of 715. There aren't many long-form Japanese texts older than this, so we can say with some certainty that, if this were a borrowing, it would have been borrowed during the Old ...
There's one I can't find much about, but I think I've determined the basis for most of your list. Here it is, regrouped a bit:
ほげ - hoge
ほげら - hogera
ほげほげ - hogehoge
ふが - fuga
ぴよ - piyo
The first three are all variations on hoge. Digging around, this appears to derive from the verb hogeru, "a hole opens up, a hole appears; to fall apart". ...