1. Tom has tomato sauce on her nose.

2. There is tomato sauce on Tom's nose.
(Are both the same?)

3. There are sinks and tall tables in the cooking classroom.

4. The cooking classroom has sinks and tall tables.
(Are both the same?)

5. The students are winning the soccer game against the teachers.

6. The students are winning in the soccer game against the teachers.
(Are both the same? Thank you for your help.)

1 and 2 mean the same, yes. (But I'd use "his" instead of "her"!!)

3 and 4 mean the same thing.

5 and 6 mean the same thing, but I'd use 5, not 6. The word "in" is superfluous.