According to the Maharshal, they simply required more baskets to carry the fruit. I will explain.

1) The Gemara tells us that 100 (not 1000) fruits could fit into a basket the size of 3 Se'ah (according to our text). Now we will do our calculations and see how big this basket must have been. We know that there are 6 Kav in 1 Se'ah, 4 Lug in 1 Kav, and 6 Beitzim in 1 Lug (these measurements all refer to volume). This means that a Se'ah is the volume of 144 Beitzim, so a basket of the size of 3 Se'ah can hold 432 Beitzim. Therefore, according to our text, 100 Ginosar fruits fit into a basket which held the volume of 432 Beitzim.

2) We must not forget the concept that the Halachic authorities mention, that "Nitkatnu ha'Beitzim" -- the eggs in our times are smaller than they were in the times of the Gemara. (This has a practical consequence for such Halachic issues as how much wine one must drink on Seder night, etc.) Some Poskim maintain that the eggs in the times of the Gemara were twice as large as they are nowadays. If we make this very approximate assumption, this would mean that the basket mentioned in the Gemara contained the volume of about 850 eggs. If 100 fruits fit into this basket, this means that each fruit was the size of 8 eggs or more, so those are pretty big fruits.

3) The above is all according to our text. However, according to the Maharshal's text a basket the size of 3 Se'ah could not hold 100 Ginosar fruits. According to the Maharshal, the Ginosar fruits were even larger than they were according to our text. According to the very approximate estimation we made above, 100 fruits could not fit into a basket which could hold a volume of 850 eggs. The Chidush of the Maharshal is that the fruits were even larger than we thought. Therefore, it must be that according to the Maharshal they required more of these gigantic baskets to carry the gigantic fruits.

Kol Tuv,

Dovid Bloom