I think if I were in your position I would go for full length (solid to the floor) partitions, it eliminates the risk of slipping under the partition, however as I type this I'm thinking about it, I'm not sure how much having a full length partition will eat into your payload, so many 3.5t can physically fit 2 16.2hh in them but their payload is only 800kg so wouldn't be safe or legal to carry those two horses, I guess it would also depend on what horses you planned to carry and what chassis you are having it built on as to weather you had excess payload that you could afford to 'give away' for just in case