In a word, yes. I don't know the specific case of Japanese translations, but I can give you other translations.

I'll start with two recent translations into English dialects because that helps demonstrate some of these more general choices people had to make, but since these are English dialect (or, minimally, dialects based off of English, depending on how you see Pidgeons and Creoles), the choices they make will be obvious to you.

Gullah is a dialect spoken on a few islands off of the Carolinas. It is, as you will see, mainly English based, but because of the large numbers of slaves and the relatively lax oversight of English-speaking slave masters, as well as their long isolation on literal islands, Gullah developed largely separately from American English, with much more influence from African languages. Gullah apparently gave us the English words nanny, yam, and gumbo, and was the native dialect of Supreme Court Justice Clarence Thomas (he once said that he majored in English at Holy Cross in part so he could finally feel like he mastered the language).

Most translations of the New Testament are funded by Evangelical missionary groups, mostly associated with the Wycliffe Bible Translators and the Summer Institute of Linguistics (they are twin organizations, with Wycliffe publishing the translations and SIL being a quasi-secular organization focused on linguistics and language learning). In the past 70 years, Wycliffe has translated into more than 600 languages, with new translations coming out several times a year. A New Testament translation is a serious endeavor, generally conducted by a someone trained at SIL in coordination with local target language speakers.

The Gullah translation came about because two missionary-translators retired to the Sea Islands, where Gullah is spoken. They had previously translated the Bible into a dialect spoken only the Caribbean island of St. Lucia. Here's what the Lord's Prayer looks like:

We Fada wa dey een heaben, leh everybody honor your name. We pray that soon ya gwine rule over de world. Wasoneba ting ya wahn, leh um be so in dis world, same like dey in heaven. Give we the food what we need dis day, yah, an eb'ry(every)day. Forgive we for we sin, cause we da' forgive dey what do bad to we. Let we don't hard tests wen Satan try we. Keep we from evil.

Notice here that they say food instead of bread. Now, the Sea Islands have bread, it's not as if in the late 20th century, these people had no idea what bread was. They're Americans. Instead, the translators chose favor dynamic equivalence over formal equivalence, that is, to give a sense-for-sense translation over a word-for-word one. In general, Evangelical missionary organizations favor dynamic translations while academics and Catholics favor formal translations but, by necessity, every translator will need to use both.

Let's turn now to Hawaiian Pidgin. The Hawaiian Pidgin New Testament, again done by one trained linguist and more than two dozen local collaborators, was published in 2000 as Da Jesus Book. Since then, they have worked on translating the Old Testament (Da Befo Jesus Book). Here's what the Lord's Prayer looks like:

God, you our Fadda.

You stay inside da sky.

We like all da peopo know fo shua how you stay,

An dat you stay good an spesho,

An we like dem give you plenny respeck.

We like you come King fo everybody now.

We like everybody make jalike you like,

Ova hea inside da world,

Jalike da angel guys up inside da sky make jalike you like.

Give us da food we need fo every day.

Hemo our shame, an let us go

Fo all da kine bad stuff we do to you,

Jalike us guys let da odda guys go awready,

An we no stay huhu wit dem

Fo all da kine bad stuff dey do to us. No let us get chance fo do bad kine stuff,

But take us outa dea, so da Bad Guy no can hurt us.

Notice here that again we see what we're used to seeing translated as "bread" translated as "food". But also note one other big difference between these two translations: while the Gullah New Testament opted for the loan word "Satan" (ultimately derived from the Hebrew word meaning "adversary"), the Hawaiian Pidgin translation opts for "Da Bad Guy".

In these cases, both these peoples were Christianized long before they got a Bible translation, such that all the core concepts are there. You might not have to coin a word for Hell (ours is from an old Germanic word giving their concept of the afterlife), or heaven (paradise is a borrowing, but heaven as in sky is an old Germanic word), or salvation (a Latin borrowing in English), and so forth.

Still, even with these long-Christianized groups, expressing complex theological concepts in a local vernacular was difficult. Here's some of the choices they made in the Gullah translation:

"Blaspheme" became "shrow slam pon": Throw slander upon.

"Sanctify" was "mek um God own": Make them God's own.

"The righteous" became "wa waak scraight wid God": Those who follow God's path.

"Grace" caused particular problems. In Gullah, the word is used in a narrow context to mean the prayer before a meal. No one knew how to render its broader meaning of an undeserved favor from God.

The Sharpes suggested "merciful favor." Greene rejected it: No grandmother she knew would say that. Finally, she came up with "blessin," as in, "We pray dat God we Fada and e son Jedus Christ gwin gii we dey blessin."

To check their work, the translators read verses aloud at senior centers. They'd ask elders to listen for jarring rhythms or phrases that didn't make sense. Then it would be back to the Sharpes' house for another round of revisions.

"Oh, my God, it was hard," said Vernetta Canteen, 61, a hotel telephone operator.

After hours haggling over how to say "grace" in Gullah, "it would be all you could do just to drive yourself home," she said. "It was so mentally draining; I don't think physical work could have been any harder."

Here's a link to the translation into Hawaiian Pidgin, here's a link to the translation in Gullah.

As you point out in your initial question, sometimes the hardest things are not the complex theological ideas but the simple metaphors. Hell and Heaven can be repurposed from preexisting terms and explained, blasphemy can be explained, but sometimes you just have to replace daily bread with daily food if people don't necessarily know what bread is.

My favorite example is Jesus as the "lamb of God". This is ultimately a metaphor tied up both with Jesus's innocence and his parallel with, and alleged replacement for, the pascal sacrifice. How do you translate that in places where they have no sheep? Sir Wilfred Grenfell was a doctor to the Canadian Island of Labrador as well as remote northern Newfoundland in the late 19th and early 20th centuries. The local Inuit (who he calls Eskimo) had already been converted to Christianity by German-speaking Moravian missionaries some decades earlier. Here's from his autobiography:

The features of the native life which appealed most to us were the universal optimism, the laughing good-nature and contentment, and the Sunday cleanliness of the entire congregation which swarmed into the chapel service, a welcome respite from the perennial dirt of the week days. Moreover, nearly all had been taught to read and write in Eskimo, though there is no literature in that language to read, except such books as have been translated by the Moravian Brethren. At that time a strict policy of teaching no English had been adopted. Words lacking in the language, like "God," "love," etc., were substituted by German words. Nearly every Eskimo counted "ein, zwei, drei." In one of my lectures, on returning to England, I mentioned that as the Eskimos had never seen a lamb or a sheep either aUve or in a picture, the Moravians, in order to offer them an intelligible and appealing simile, had most wisely substituted the kotik or white seal, for the phrase "the Lamb of God." One old lady in my audience must have felt that the good Brethren were tampering unjustifiably with Holy Writ, for the following summer, from the barrels of clothing sent out to the Labrador, was extracted a dirty, distorted, and much-mangled and wholly sorry-looking woolly toy lamb. Its raison d'etre was a mystery until we read the legend carefully pinned to one dislocated leg, "Sent in order that the heathen may know better."

Kotik, other versions of the story tell me, is not just a white seal, but a baby harp seal (see pictures here) which seems to be a very apt local substitute for lamb.

Those are always the choices you're going to have to make: do you make God "Gott" as it is in German or do you say something like "great spirit", do you translate "bread" as "bread" or "food" or "rice", do call Jesus the baby harp seal of God, killed so that the faithful may live forever? The simple answer is that translators make different choices, but you certainly do see some non-literal translations that seek to give a clear sense of the meaning rather than merely straight translation of the words.