The MTU has nothing to do with LACP.
It might be that the packets crossing the links are big, should not be fragmented and they are dropped hence keeping the links underutilized. But in this case, you should see problems with the applications.
The 'low' throughput might be because the applications are using relatively small packets.
Keep in mind that what you see as line rate is different for packets at 64B and for packets at 1500B.
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If this worked for you please flag my post as an "Accepted Solution" so others can benefit. A kudo would be cool if you think I earned it.