I am really struggling to imagine a likely scenario where pants ONLY means long legged pants. Maybe in some formal setting (this board does skew older and more formal probably).
“Not wearing pants” = only underwear or less.
Unless it’s a hot young woman about 1/3 my age, I try not to visualize it.
I think I would picture them in either pajamas or boxer shorts, assuming the person is male. (Maybe I shouldn’t assume this, but I’m having a much harder time imagining a woman saying this – both because most women have learned the hard way never to say anything their audience might construe as sexually suggestive unless they WANT it to be taken that way, and because it’s very common for women to both be “not wearing pants” and within the normal bounds of professional dress, so it doesn’t really make sense as shorthand for “not dressed for the office.”)
It means . . . FREEDOM!
There’s an annual event called the No-Pants Subway Ride, and it’s definitely people in their underwear, not naked and not just wearing shorts or skirts instead of trousers.
Pants. Underpants. Underpants go under pants. No pants only underpants. Quad Erat Demonstratum
I basically agree with Alessan. Context matters. If my mom calls and says she’s coming over and I say “ok. I better put on pants”, that doesn’t mean I am sitting around in the literal all-together, it means I am not suitable for company and need to get myself into something at least mom-presentable. On the other hand, if I say “the best thing about quarantine is I haven’t put on pants in 4 months,” I mean I haven’t put on work pants, or even the less comfortable sort of jeans.
It’s not. 
Then it won’t mean anything to me. 
In some countries, pants specifically refers to underpants, and “trousers” are pants.
To me the OP just means they’re more casual than they would be at the office. Right now I’m wearing PJs. There is no way I would go to the office in these. If I lived by myself I could do my work wearing only underpants in this heat, but that would make things awkward if there was a delivery (sometimes they don’t drop the stuff by the door, which I think they’re supposed to).
I suppose it means whatever you want it to mean. In my case, it’s usually either pajama bottoms or a kilt.
I agree. As evidence, I would point to the existence of capri pants, which are between short and long pants. Pants are pants, regardless of the length.
To me, it means “I am not wearing bottoms that I would wear to go outside.” So either you’re just wearing underwear, you’re wearing nothing, or maybe some kind of pajama bottoms.
What I picture when someone says they aren’t wearing pants is a guy who looks dressed from the waist up but with only boxer shorts.
Another unnesseary repeat of the fact that context matters. In normal situations the person could be in shorts, a skirt, a dress, their underthings, or their altogether; any could apply. But if a person is proudly announcing that they’re using their isolation to get away with pantslessness, I don’t take that as wearing jorts.
It means wearing anything except pants, which includes wearing nothing. Definitions of ‘pants’ may vary.
It means that if they needed to run to the store, they’d need to add clothing or change clothing. So, it could be pajamas, or underwear, or commando, or the things that you only wear around the house.
If I were to knock on their front door, they’d need a few minutes to pull themselves together.
It’s a comment I don’t dig too deeply into.
Or it might mean you were not wearing pants, but you were choosing to wear something protecting public decency, like a skirt. Duh, nice, potentially leaving out 51% of the population (plus other societies and cultures which adopt non-pants clothing. Ethnocentric, gender centric much?)
I voted for underwear, but based on what people I know who have made this statement have elaborated it could also mean they’re wearing shorts, pajama bottoms, or sweat pants. So far it has never meant naked from the waist down or wearing a skirt.
A-ha. 
It means underwear at the most and possibly nothing.
“Feels like I’m wearing nothing at all…”
“Stupid sexy Flanders.”