Every strong acid,strong base reaction has the same net ionic equation correct?
I suppose, but that won't help you here, since you will have to use the molarity of the the actual reagents.
Why won't M1V1=M2V2 work for this problem?
No. I suppose you could test that by filling all the values in your formula, if you're missing too many, then you'll know it won't work.
I assume the ratio of moles isn't one to one (or is it), but if the net ionic equation is the same...
You'll know when you balance the equation
2HNO3 + Ba(OH)2 --> Ba(NO3)2 + 2 H2O
Good. Now, you have a balanced chemical equation. What are the units understood in a chemical equation? There are some units understood to be there, 'tho this is somtimes hard for a new student to see.