I think there were a lot of reasons for the rather casual data collection of names and dates. 1) The people being counted in the census may not have been literate in the first place and may not have known how to spell their names. So the census taker wrote down whatever phonetic spelling made sense to him.
2) They may have been from a part of Lithuania where records were kept in Russian, and what little reading and writing they knew might have been in the Russian alphabet. As you may know, Russian doesn't use the same character set that English uses, and they might not have known how to translate the Russian letters into English equivalents.
3) For Lithuanian Catholics, records were in Latin and names were transcribed in their Latin equivalent. There were no birth, marriage, or death certificates. For Christians, the church made records of baptisms, marriages, and burials. There were no civil records, only religious ones. (For Lithuanian Jews, records were in Hebrew and made by the rabbi.)
4) As people still sometimes do when their country is occupied by another country, I know Lithuanians living in Europe tried to fit in or "pass" by Russian-izing or Polish-izing their surnames.
5) The purpose of the census wasn't really genealogical -- it was for statistical, political, or research purposes. The census taker's job probably wasn't really to get the names spelled exactly right -- it was to count noses.
6) The concept of a "legal name" is a relatively new one. In some less developed countries, there's still no such thing as a legal name.
7) These days we have lots of things with our names on them -- bills, drivers' licenses, credit cards, etc. In the 1800s, people didn't have such documents and didn't carry around papers that had their names on them.
Basically, until the fairly recent past your name was what your family called you and what you called yourself. Period.