According to Super Smash Bros Wiki, Olimar's damage is stacked up by the different colors of Pikmin. Each color of Pikmin has it's own variety of skill sets and advantages. The purple Pikmin is the only color of Pikmin Olimar will pull for the Home Run Derby which would explain the difference in power compared to a normal match-up where Olimar would pull more than just purple Pikmin.
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Edit: To further answer the question. Olimar's physical weight/gravity is not affected by Pikmin however, the weight in damage is reflected through the variety of traits that Pikmin have depending on their color.
The number of Pikmin do not affect the Home Run derby due to the Purple being on the stage and will always be last in line.
The number of Pikmin do affect the normal battle because of variety of colors that are available and each color of Pikmin having different traits.