1. There is no difference, but "these days" often implies a longer time span:
- These days, apartments in Seoul are expensive.
- Kids these days are disrespectful.
2. Basically no difference, bit "in it" can also mean "mixed into" the other ingredients:
- My coffee has cream in it.
- My bread has raisins in it.
"Inside" can only mean that the beans and custard are in the center of the pastry, and not mixed into the batter.
3. Very little difference. I guess = I think, I suppose, I presume. Probably = it is likely.