Yup making cycling at full cost the better option (as you describe tackling the issues around safety, theft) will have a real long-term impact, otherwise you might end up subsidizing a fun little toy that is used for a few weeks then goes back to the garage.

Another problem with subsidies is that it targets a specific mode (e-bikes), while simpler, cheaper, normal bikes might be good enough already. It could also lead to local sellers increasing the price of e-bikes.