Could be. 16 months is a long time, although 11,000 miles isn't far.
Can you do this yourself, or know someone that can? It's easy, and not
very expensive if you spin your own wrench. I would NOT recommend a flush
unless the trans has been serviced regularly over the course of it's life,
and even then, I shy away.

Clunking sounds rarely go away by themselves and tend to get worse over
time.  Toyota automatic transmissions rarely make clunking sounds so I
suspect that the source of the sounds is not the transmission.

There is a screen in the automatic transmission, but unless the transmission
is badly abused and on its last legs, I've never seen it get clogged.
Automatic transmission fluid should be changed in accordance with the
maintenance schedule in your owner's manual.  If it has been over 60,000
miles since the fluid has been changed, then do not get it flushed - just
drain and re-fill the fluid.

Lots of things can cause clunking sounds.  If the brake pads are
aftermarket, they sometimes clunk when changing direction from forward to
reverse and vice versa.  Other potential sources of clunking sounds are
constant velocity (CV) joints, wheel bearings, struts and strut mountings,
and loose and worn steering and suspension parts like ball joints and rack
ends.