Yeah text editors tend to mess up formatting/remove things they did not expect- another reason text editors are not so good for actual editing. Fine to create things to copy and paste with but straight editing is a more risky proposition.
ShiftJIS roman vs ASCII- best thing is to replace like with like. If however it works as you say and does not crash or decode incorrectly by all means have at it and use 8 bit characters all you want- if it was just the odd control code or something that was overwritten that caused crashes then that is great.
You have picked a very odd game to learn to translate with, nice as it covers quite a bit and is fairly logical but still odd compared to what we usually see.
Some waffle
I noticed both types mixed in there but I did not look to see if such things were limited to one thing or another.
For example the game over sections were very short and in plain ASCII where others that had markup (things in square brackets) opted for ASCII and other sections opted for straight shiftJIS including the roman characters they may contain- lines around 136 in text_jp are the "function name"={text} with the {text} part in ASCII.
There is likely method to the madness but it is probably masked by the game (it expects certain sections to be in certain formats) rather than being something very simple you can see easily in the text file when you are looking at it- it is then easier to do the like with like thing to spare headaches there (assuming you do not need to change the font for something both methods have Roman characters and so both are acceptable).
In essence you can then consider it a dual table game (a game with two ways of encoding text).
Yes most games force 16 bits even if the standard they are supposedly using (for instance shiftJIS) will support some measure of 8 bit characters (although that quote was not aimed directly at that- that was more to say that even if the text is 16 bit the control codes like new line, make the following section bold....... can still be 8 bit which can confuse things like hex editors and simple text parsers)
I also sense you are not quite getting what pointers are- simply put they are like a contents page or an index in a book. Chapter 5 is page 50 sort of thing except usually it is just a hexadecimal number*.
I suppose technically this arrangement can count as pointers but it is very rare for things to be done this way (I am struggling to think of another example at this point for a handheld or 16 bit/older game).
The naming a section and having it copied or parsed is closer to a variable or even a function than a simple pointer (I saw many of the same things when I was looking at other files though so technically they can count as pointers, it is not a very efficient way of doing things but I guess if it works and does not slow things down too much all is good).
*pointers are used everywhere in games- games will use them to point to places in memory for text, for graphics, for values the game needs (indeed such things can trouble cheat makers), all but the simplest sections of actual code will use them (the other two methods involve things at the instruction level or in other registers), files will use them to point to later parts of the file (many of the big sound hacks a simple edits of these), the hardware itself uses them to keep track of code (see stack pointer) and it goes on.
ShiftJIS roman vs ASCII- best thing is to replace like with like. If however it works as you say and does not crash or decode incorrectly by all means have at it and use 8 bit characters all you want- if it was just the odd control code or something that was overwritten that caused crashes then that is great.
You have picked a very odd game to learn to translate with, nice as it covers quite a bit and is fairly logical but still odd compared to what we usually see.
Some waffle
I noticed both types mixed in there but I did not look to see if such things were limited to one thing or another.
For example the game over sections were very short and in plain ASCII where others that had markup (things in square brackets) opted for ASCII and other sections opted for straight shiftJIS including the roman characters they may contain- lines around 136 in text_jp are the "function name"={text} with the {text} part in ASCII.
There is likely method to the madness but it is probably masked by the game (it expects certain sections to be in certain formats) rather than being something very simple you can see easily in the text file when you are looking at it- it is then easier to do the like with like thing to spare headaches there (assuming you do not need to change the font for something both methods have Roman characters and so both are acceptable).
In essence you can then consider it a dual table game (a game with two ways of encoding text).
Yes most games force 16 bits even if the standard they are supposedly using (for instance shiftJIS) will support some measure of 8 bit characters (although that quote was not aimed directly at that- that was more to say that even if the text is 16 bit the control codes like new line, make the following section bold....... can still be 8 bit which can confuse things like hex editors and simple text parsers)
I also sense you are not quite getting what pointers are- simply put they are like a contents page or an index in a book. Chapter 5 is page 50 sort of thing except usually it is just a hexadecimal number*.
I suppose technically this arrangement can count as pointers but it is very rare for things to be done this way (I am struggling to think of another example at this point for a handheld or 16 bit/older game).
The naming a section and having it copied or parsed is closer to a variable or even a function than a simple pointer (I saw many of the same things when I was looking at other files though so technically they can count as pointers, it is not a very efficient way of doing things but I guess if it works and does not slow things down too much all is good).
*pointers are used everywhere in games- games will use them to point to places in memory for text, for graphics, for values the game needs (indeed such things can trouble cheat makers), all but the simplest sections of actual code will use them (the other two methods involve things at the instruction level or in other registers), files will use them to point to later parts of the file (many of the big sound hacks a simple edits of these), the hardware itself uses them to keep track of code (see stack pointer) and it goes on.
Or others 
. Saves on time, soap, water and money having to wash them.