Will your DS be going into year 6 or year 7? And what year for your DD?
If your DS is going into year 7, and he will be boarding for the long term not for 1-2 years, you might also look at senior schools that start at year 7 (or that have their own junior school attached).
There are a lot of very good boys prep schools, but you need to think about what you want. Some of them are kids aiming for the large 13+ school (e.g. Eton, Harrow). These children will have been on this path for quite a while, and will pre-test in year 6. So if you are joining in year 7, your son might be looking at different destinations schools compared to his classmates (not necessarily, and a good head will be able to advise). Some more traditional boys prep schools are Sunningdale, Cothill, Aysgarth (in the north), Woodcote House, Pappplewick etc.
Somewhere like Ludgrove is good in that all the children board together, but that school is fortnightly. For any school, check how many children board on a Saturday night. In particular, how many of your child's age and sex. Frankly "how many year 6 boys boarded last Saturday" is the sort of question you want to ask.
You are right that there are not many girls' boarding preps left, most junior girls who board are either at co-ed schools or in the junior boarding division at all-through schools. Some senior girls schools that have junior boarding provision include Godolphin (Salisbury), Badminton Junior, Thornton College, Adcote School or Royal Masonic School for Girls. These may not suit your requirements, I am just putting the idea out there. I don't have any experience of these particular schools. But also note that the number of boarders usually increases year-on-year in these types of schools, number can be very low at the junior end, especially at weekends.
Another all-through school with a junior boarding option is Moreton Hall, which starts boarding at year 3 and is co-ed in the prep school, and then girls only from year 9 in the senior school (that might change, the age of boys allowed there has been creeping up over the years). If you look at co-ed, all-through schools (meaning prep + senior), there are many, many options. But, for example, drill down on the numbers. Some of these schools will have thriving sixth forms or 13+ boarding, and will say they have 400 children board every weekend. Then by the time you look at, say, the girls junior house it turns out they have four girls in every weekend and only two in your daughter's year group.
Having said that, Hanford and Godstowe are both very good preps if you do want a girls' prep school rather than all-through.
If you are looking at full boarding to start and then weekly in the future, geography may become a significant consideration (the schools should be near your home, or somewhere you could happily move to, and if the children are at different schools, close enough that they can both come home at the weekends).
I'm not sure if you're a military family, but one tip I have is (whether you are or aren't one yourself), look at schools that take children from military families on Continuity of Education Allowance (CEA). These children are more likely to be English speaking full boarders, and the school will be used to providing proper full boarding. The MOD used to have a school finder website, I can't find it now but there is this directory that shows schools that take CEA pupils: https://www.directoryofboardingschools.co.uk/boarding-schools-2022
Co-ed preps I have heard good things about are Windlesham House, Hazelgrove, and Highfield and Brookham (the last one is the name of one school not two). However, I have not been much involved in the prep boarding world for a few years now, and schools can change enormously in a few years. I suggest once you have a shortlist, you should post threads with the school names in the title to get up-to-date information from parents.
For any school, look at the things that will really matter: pastoral care and safeguarding would be number 1. Really drill down on this - different schools have different policies and you may be surprised what bothers you. For example I have worked in a girls school where men were not allowed in boarding - for example both the matron and a gap student had to supervise the plumber who came to fix a shower. At the other end I have seen schools where the head of junior boarding was a man who had unsupervised care over young girls.
Speak to any parents you can. If you pick prep rather than all-through, leavers' destinations are very important - you want broad opportunities, year 9 will come faster than you know. Make sure you know the "pressure level" at the school. I have seen schools that publish weekly or fortnightly rankings of the class - alternately I have seen schools that won't even host an annual prize giving. And if your child has one or two hobbies they love, please pick a school that offers them - it's not like a day school where you can make it up in the evenings.
Check how the school functions - are girls and boys kept separate at co-ed preps? Are the sports options different - no point sending a cricket mad DD to a school where only boys are allowed on the team. No point sending your kids to a co-ed school to support each other if they are in separate houses and only see each from a distance. Also check on some things e.g. I have seen schools where the choir is almost entirely girls and this has put talented boys off. They may be better off in a school with less of a choir provision but a better boy/girl mix or boys only. Doesn't matter how good the choir is if your kid won't participate.
I would also say make back up plans. If your child comes home and says "Mum (or Dad) I can't do this, I thought I was ready but I'm not and I don't want to go back," - then you need to have something in place.
With your children it can sometimes feel like you have limited options - e.g. looking for junior all girls boarding for your DD. Don't fall into the trap of thinking this way. Junior boarding is a "buyer's market" as there are more options than children for all but the most exclusive schools. Finding the right school for each child is more important. You want to make sure that the child fits in well and loves it. Most schools will bite your arm off for a junior full boarder - make sure the school is right for your child.