Binary Classification Comparing two time series of variable length
I think both LSTM and 1D-CNN could work, but it depends on your data first.

In your code you used a shared LSTM, which implies that you think your two input sequences are actually just different length sequences of a same variable? If that's the case, why not just use a LSTM to label, and then compare their label.

If that's not the case, you can then use separate input.

So the restriction for using 1D-CNN for sequence is that your sequence should have same length among samples (to my current knowledge). So if you have two types of sequences with fixed length $l_1$ and $l_2$ among samples, then you can try this approach.

If your have two types of sequences, both with variable length, then you will have to use one dynamic input LSTM for each of them, and then concat this two LSTM.