Every Vietnamese restaurant I've eaten in (in the US) uses jalapeno peppers in their pho. I assume that's an American adaptation to the dish. Is that correct? If so, what kind of peppers are used in Vietnam?
Chilli is a strictly optional condiment to phở and many Vietnamese will eat theirs without it. In Vietnam, if fresh chillis are served, it will likely be one of two types:
Ớt sừng trâu, literally "buffalo horn" chilli, large and fairly mild. One of many cultivars of C. frutescens, typically sold in the US as "Red Cayenne" although that label is unfortunately also applied to many other chillies as well.
Ớt hiểm, aka bird's eye chilli, small and very spicy.
Not coincidentally, there are also the two most common varieties of chilli eaten in Vietnam.
Jalapeno peppers are somewhere between the two: a C. annuum cultivar like bird's eye, but not nearly as spicy. To my taste, using this is a far lesser sin than getting the other herbs wrong.
I'd go with Bird's Eyes, or as they're sometimes called, 'finger' chillies.
I'd define it as skinny, thin skin, lots of seeds - finger tend to be larger, green; bird's eye smaller, red.
The trouble with chillies is that they can all look a bit alike & trying to buy one very specific type is really not easy. Is it a jalapeño, is it a fresno or a serrano… what's the real difference? Can you tell just by looking, or even tasting?
You can easily tell the difference between a scotch bonnet & a jalapeño, of course, not only do they look completely different, they taste & smell completely different, but a lot of the others come in much finer distinctions.
Finger chillies & bird's eyes are close to being the same thing. They're not identical, but to the consumer it's really tough to tell them apart. Supermarkets tend to call the larger ones finger & the smaller ones bird's eye - they taste the same. See https://www.sainsburysmagazine.co.uk/lifestyle/food/a-guide-to-chillies for how the supermarkets very, very broadly differentiate.
BTW, I can tell the difference between a jalapeño & a fresno… but not if the ones the supermarket is selling this week look like something half-way between the two.
Late thought - cayenne looks like a 'finger' variety too; All I can think is they call them finger if they're green & cayenne if they're red. They never really tell you exactly what they are.
Until I moved to the western US, I would see Pho with thai chiles (which they seem to call birds eye out here), and only started seeing Jalapenos after moving west. I've seen thai chiles in Pho at a few places around in Utah, but Jalapenos are the most common. I'm not Vietnamese, but it sounds like it's a southern vs northern thing. Southern Pho is more often to have seranos or jalapenos and northern is more often to have thai/birds eye chiles in them. However if you've gotten a good broth you probably won't go wrong with either. While I like thai chiles my wife can't stand them, they're quite hot (almost as hot as Habaneros).