The essential difference is in specialization between these two. Sequencers are intended for use in making detailed MIDIs and then outputting them through a sampler with some nice sounds loaded to produce the final output audio file. Notation software is intended for use in making sheet music; beautiful, accurate musical scores.
You can use a sequencer to make scores and you can use notation software to sequence MIDIs but each one has specific tools and specializations that make it better for its originally intended use.
More recently, the line between the two has begun to blur as notation software is adding more advanced MIDI controls and coming with samplers built-in and sequencers are gaining more advanced notation tools. Eventually they'll just be more or less the same thing.
Hope this helped
