The first inn in the first Dragon Quest/Warrior game, where you can take the girl and spend the night. You can also take both the village girl and the princess and have a threesome.

There are also a few naughty jokes in Link's Awakening. "checking other people's chests," picking up Marin, and originally the mermaid's necklace was her bikini top. 

Going with super paper Mario where that guy tries to cyber peach then you take control of peach and put him in his place.

The lady in red that restores Link's health in Zelda II by taking him inside her house for a quickie:

Pokemon, the paper mario series and other Nintendo games with a good amount of text dialogues had lots of them

On a related note, we all know what really happens when Link signs up for the "special" massage at the Gerudo Inn.

A yes that thing was an animated gif from a pokemon sequence from imgur, but i think they a supposed to play as videos called gifv, so i don't know how to embed them

Some other that might count are

there may be other quotes from PMTYD and others in that series but i would need to do a better search since there is a lot of text

"I don't know about this...It's awfully tight. And it kind of smells a bit..."

Shantae series has a lot of snarky dialogue both from main characters and random npcs since the first games:

"My mom dressed as the pirate lady for dad. But I'm not allowed to say such things." (the pirate girl "risky boots" just like other main characters from the series dress in a very risky way) 

"Sometimes I wish I grew up to be a dancer instead of a jug holder."

Shantae raids Risky's wardrobe:

Talking to a little boy NPC at the  beginning  gives:

NPC: Body armor is critical in battle! It should cover a warrior from head to toe. Just… not the arms. Or legs. Or the mid-section, really. Ideally not the face either… knees or elbows.

But i don't know if this series would still qualify as kids games since later games despite being a bit more cartoony in some areas, are getting more and more direct with the suggestive content

Same for Fire Emblem, I don't know if still qualifies as a kids game since they have some very mature elements, and the ratings have been rising in the classifications, but Niles in FE Fates is a goldmine of "double entendre" phrases in his support conversations, Fire Emblem Heroes has recorded lines and texts that could also be easily missinterpreted out of context.

I like how Majora's Mask always stops just short of admitting that Chateau Romani is an alcoholic drink.

On a darker note, if you complete Romani's and Cremia's quests, Cremia is clearly using Chateau Romani to make sure Romani is good and doped up so she'll sleep through the crash of the moon.