I am going to guess that you are trying to approach factor-based SEM from some older texts where factors tend to be orthogonal. Take a look at the "lavaan project" tutorials:
I think it will be clear that which covariances are estimated and which are constrained to 0 is up to you. Generally speaking, if a nonzero covariance offers a better fit to the data, but yoor model constrains that covariance to 0, thsi will tend to be reflected in lack of fit. Collinearity has the same effects in factor-based SEM as in regression, but remember that collinearity invoves multiple predictors for the same dependent variable. In a common factor model, observed variables are often dependent on ony a single common factor (and an orthogonal unique factor or error term), so there is no collinearity.
This is a very general SEM question, so it is better suited for a general list like semnet: