So is vin word the same as kaffe and öl I mean we can say vinen when we are speaking about a bottle or a cup and say vinet when speaking about wine in general
This works to different degrees with different nouns.
Both en öl and ölen work fine. We normally say en kaffe about a cup of coffee, but not kaffen about that same cup in the definite form. And for wine, we don't even say en vin.
What I said here is true for general usage. The jargon among wine afficionados, restaurant staff etc is another question, people who specialize in something will always express themselves in ways that differ from the average usage.
No, not really. I've never heard anyone say "vinen", it's just not idiomatic. You'd say ett glas vin or en flaska vin.
People actually say it when talking about lådvin. It sounds absolutely ridiculous to me, but... it does happen. Maybe the boxes are perceived as more quantifiable than the bottles, I don't know.
Perhaps that is so... I'd say vinet about bag-in-box wine as well though. Nonetheless vinen is a lot more uncommon than ölen.
Is true that the nouns taking en as modifier now take suffix en and no countable nouns take et?
The first part has some truth in it: Many en nouns will have the -en suffix as definites. en bok, boken 'a book, the book'. But many others will end in -an. en klocka, klockan 'a watch, the watch'.
The last part is not true. Many ett nouns are countable. ett äpple, två äpplen 'an apple, two apples'.