I cannot understand shipping Sonic (or any character) with another character being inherently viewed as disgusting or discomforting, unless the nature/reasoning behind said ship is explicitly stated to be sexual in nature by the poster, or is shipped only for the shippers own sexual fantasies.
If you inherently attach sexual relations to a ship anytime you see it mentioned, then you clearly are not very knowledgeable in romantic relations to begin with. Someone can be asexual (i.e. have no desire for sex), but can still be incredibly romantic (i.e. have a strong desire to be in a romantic relationship). Conversely, someone can be extremely sexual, but aromantic (have no desire for a romantic relationship). And any other derivative is possible too - someone could be really sexual but still really romantic! It should also be noted that kissing lip to lip, even for an extended period of time, is not inherently sexual. Heck, kissing is pretty much how you say "hello" to a friend in French!
As far as shipping Sonic in particular goes - if you ship him in a sexual manner, it's purely for your own desire, because Sonic in the video game canon has never implied that he has any sexual interests (all joking about his "SUPER 69 ATTACK" with Tails in Sonic 4: Episode II aside). You are perfectly entitled to do this, but as far as expressing this around here goes, you're best not doing it, because many people are uncomfortable with anything involving "sex" and "animals" being put together.
However, as far as romantically shipping Sonic goes, it's perfectly in line with in-game canon. He has never been in a romantic relationship, nor has he never explicitly claimed to be interested in anyone romantically. However, he cares a lot about Amy, and his care for her isn't exactly in the same vein as his bromance relationship with Tails (another character he cares for deeply), and he often goes out of his way to protect her (even though she is capable of handling herself - and even though he knows that first hand). There are some elements of his care for Amy that could imply romantic interest. And there is also an implied romantic interest (and a definite romantic chemistry) between Sonic and Blaze in the Sonic Rush games (though the "interest" is more on Blaze's side).
And one key thing about Sonic is that he has an amazing sense of empathy. He's very good at understanding the feelings of others. That's perfect for involving him in ships.
When it comes to Smash Bros shipping, it's really part of the fun of the game, and Sakurai himself clearly has fun with this:
The Smash shipping fandom is as officially acknowledged and approved as the competitive community. And just like no character is left out of a tier list, no character should be left out of shipping. While I think some restraint should be shown with sexual ships in terms of when, where, and how you express them, everything else is fair game.
In terms of crack ships, all that matters is that the ship is silly and cute in some way. In terms of sexual ones, all you need is to get turned on by the though of these two characters getting dirty - but that's not something that's appropriate to go into detail on around here. In terms of more serious ones though, just make sure it fits in with the canon portrayal of the character. For example, Peach and Link work in both a "crack ship" and sexual context for many people - but is it in any way
realistic according to their
actual canon portrayals for them to fall for each other (I'm not saying Link x Peach is unrealistic in a serious sense, and I'm not saying people who ship them like that are ignoring canon - I'm merely posing the question, as an example)?
Of course, you can ignore canon ships for Smash because it's a bit too limiting a thing to adhere to in the case of some cast members (e.g. Mario and Peach, who are in a romantic relationship in canon, and even worse, with each other). But you have to take the overall canon personalities and qualities of these characters into consideration, if you want to seriously think about certain ships. Crack ships can go anywhere though, and are often designed to break canon portrayal rules (Ganondorf and Jigglypuff would NEVER fall for each other, but it's still hilarious to think about them being together, hence, they are a crack ship).