Yes, those small square planters are very restrictive as far as giving adequate room for rootmass. They are really only productive if you are growing from small clones, otherwise they tend to stunt growth and thus reduce potential yield.
Modifying them to have more holes around the sides near the bottom is a must, it will encourage a nice healthy root mat in the tray around the planters.
Building a cover plate to suspend the square planters over the tray will allow the roots to freely flow out of the planters without any possible damage caused by the weight of the planters sitting on the root-mat and blocking the holes. (similar to picture below)
Better yet, use orchid pots or net pots, suspended over the tray by a cover plate with holes cut to place the pots thru.
The suspended planter or *orchid pot method provides the maximum for root mat development. The optimum root mat develops when a modified orchid pot co net pot is used.
Modified (left) and standard (right) Orchid pot co netpots
*Orchid pots are heavy duty net pots made by the Orchid pot company, they are better than ordinary net pots because they have a flange molded into the top of the pot, allowing for the net pot to be suspended in a hole without the risk of the combined plant/pot/rocks weight causing it to fall thru the hole. Orchid pots are available from grow stores and they usually sell for about $1.50 each (10 for $15.00), good cheap and easy to use.
The modified net pot allows for superior root growth and prevents common root damage which can happen when the roots hang down over the sharp edges of the plastic net pot openings.
Another option is to simply fill the entire tray with grow rocks and forget about using any pots or planters, this will give an adequate root growth space. *Almost as good as the suspended orchid pot method.
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See also
DWC conversion of ebb & flow tray systems