Hi, your second guess is right - not ECN-capable transport means ECN is not used in this connection.
If it were used you'd see 10 – ECN Capable Transport, ECT(0) or 01 – ECN Capable Transport, ECT(1). In case of network congestion AND if ECN is used you'd see 11 – Congestion Encountered, CE.
Value of 00 is quite common in general purpose networks outside of datacenters.