DXB transfers between T2 and T3 aren’t fun, but Emirates does this all day long. If it’s on one ticket, they wouldn’t sell it if it was impossible. Arriving early helps, but I wouldn’t count on it.
At check in, definitely tell them about the short connection. Sometimes they’ll flag it, seat you closer to the front, or at least note it in the system. Also move fast and follow the transfer signs immediately. No wandering.
If the inbound is late, Emirates is usually pretty good about protecting the connection or rebooking, especially for long haul like Tokyo.
I wouldn’t stress too much, but I also wouldn’t relax until you’re at the T3 gate.
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