With regard to your 2nd question, Sims that already have maxed a skill or career don't get any points for that. You'll want a housemate at level 9 of a skill or career.
So does this mean if you start with a founder that has level 9 in a skill would they already have 9 points from that?
My understanding is that you can only count points for things achieved once the founder/heir moves out, so you would not get 9 points for skill levels your Sim has prior to moving out but you would get the 2 points if they max the skill.
There are two categories that cover skills, the designated skill and the 2-pt maxed skill. Any Sims can claim the 2 points, regardless of whether a skill is designated. The designated skill must be unique.
Example: Founder chooses piano as a designated skill. Every level of that skill gained after moving out counts one point. If the skill is maxed, you get the other two points for maxing a skill.
Your heir cannot use piano as a designated skill, but could still max it for the 2 points only. They have to choose a designated skill different from the founder and any previous heirs.
No one may use cooking or handiness as a designated skill, but all would get the two points for maxing.
Does building a second storey on a house count as changing the blueprint if you make the upper level look exactly the same as the original level, as in you keep the same shape?
Can founders or heirs take objects they have earned from events with them when they move?
I'm not sure about the first question, but I think you would not be able to add a second story. You can add a basement, though.
Founders and heirs can take anything they find or make with them. Objects earned from events--you mean date and party rewards, I assume--can't go in the personal inventory, so could not be taken.
Just so I understand the skill points thing, if a heir were to gain 5 points in a skill but not max it, that means another heir can max that skill and get the additional 2 points from it right? Would they still get the first 5 points from that skill?
That depends on whether it is being counted as a designated skill. I think my answer to your other question covers this, too. Again, I am not a team member, so whatever I've said isn't official. I'm sure
@MarianT will correct me if anything I've said is incorrect.