"Can anyone speculate to why they might have done this/is it common?"
If you're talking 1700s then different spellings are very common indeed. For example, one ancestor of mine by the name of "Wixey" I have found four different contemporary spellings of the name between 1720 and 1770.
My ancestors back then were, more often than not, illiterate farm workers who signed the marriage register with a mark X rather than signing their name. The spelling of their name was entirely down to what the local vicar thought it should be.
This even occurred into the 1800s as well. I have a relation who worked as a tailor and whose last name had always been "Barlow" but then in the 1840s he just decided to change the family name to "Barley" for some reason. All the children were baptised as Barlow but in the censuses the family gave the name Barley. Who knows why?
"I found some classically ashkenazi first names around then so wondered whether anti-semitism might have sadly played a part?"
and
"...I'm waiting on the results of a DNA test..."
I can't speak to anti-semitism but if you come from an ashkenazi background then you are very likely to find a lot, and I do mean a lot, of DNA relatives.
In genetics there is something called "endogomy" which is where the same extended families tended to intermarry over several generations. You can then still see the results of this in the DNA hundreds of years later.
It is not uncommon for Ashkenazi Jews, Puerto Ricans, colonial Americans, French Canadians and US Cajuns to have large numbers of DNA matches due to endogomy many decades or centuries previously. The same thing applies to certain communities from South Asia as well.
If I can tell you a story. When I did a DNA test (actually my mum & dad did them as well) it came back that my mum had loads of people who were shared matches with her and each other. And they all, absolutely all of them, lived in the USA (we live in the UK) and most of them have ancestors going back in the USA to at least the early 1700s.
It turns out that my mum had a couple of distant relations that went over to America in the 1600s. To be frank, there was a lot of families intermarrying each other back then (the population in Maryland and Virginia was very small) and you can still see the results of that in the DNA today.
Many Americans who trace their ancestry from that time have found this when getting their DNA results. I remember somebody saying that they had colonial ancestry from Maryland and Virginia through both parents, and while the parents weren't related to each other they had dozens of DNA matches on ancestry who were related to them through both parents, and quite a few more who had a DNA match to one parent and a paper trail that connects them to the other.
It may be that you will find yourself in a similar situation.
"For finding historical records could you recommend the best site? I have a MyHeritage at the moment as I'm waiting on the results of a DNA test but prepared to move to another website if there is a better one"
I don't think that there is one "best" site. They all have their advantages and disadvantages.
I have subscriptions with Ancestry, FindMyPast and MyHeritage. It depends what country you're looking at.
MyHeritage seems to be quite good with the US and some European countries, not so good with the UK. Ancestry is generally good all round. FindMyPast is good where Ancestry is weak and I find they complement each other.
If I could only choose one of those then it would probably be Ancestry. Although, for context, most of my family searches are UK related or those that emigrated to America, Canada, Australia or New Zealand. However, if you are looking for records from multiple European and other countries then MyHeritage is usually very good indeed.
Ancestry is also the easiest site to use to do a family tree. I found it a lot easier than trying to use MyHeritage.
The big issue with Ancestry though is that you cannot upload DNA from another website - you have to get an Ancestry DNA test. The standard price is £89 but they do special offers from time to time, it would probably be best to keep an eye out for those.
Just checked, they had a special offer over Mothers Day for £69 so it's likely that they'll do something similar in the near future.