All 60s Omegas I`ve come across have had the logo in the glass (provided it's a genuine Omega glass). Can`t be 100% certain with the Speedmaster but I think it would have the logo at this age.
If the one you've got doesn`t have the logo it indicates that the glass is probably a generic. If it's in good condition, fits/looks OK and it's keeping the wet out I wouldn`t worry. The only advantage with the genuine glass is knowing that it'll fit correctly and look right; if a generic meets both criteria it'll do the job just as well..........the Omega logo is only significant when selling a watch!
A genuine Omega glass is around £22 + fitting.
Paul