Schools will still have SEN departments, although I know of one school which proudly advertises that it doesn't and advises parents to go elsewhere if their child has SEN.
The issue is with LA funding of children who can't attend mainstream schools. Even with academies, LAs have been allowed to keep back a small sum to fund administration of admissions, SEN, transport and safeguarding. LAs are expected to step in if a school is in serious difficulties, even if it is an academy.
It's not directly linked to academies, but the amount LAs have been receiving for SEN has been shrinking, so funding for special schools has been increasingly hard to find. Many special schools have closed, so children have often have to travel miles to attend a specialist school, even if the parents can find a place.
Mainstream schools often fund their special needs departments out of general funding. Academies, which are in control of their own admissions policies, have no incentive to provide support for SEN pupils and they will almost inevitably drift to 'sink' schools.
Local authority funding for and provision of in-service training has been almost non-existent for years. Academy chains provide it on a 'do it our way or else' basis, which is what the worst LAs did years ago. Grant maintained schools have always been able to buy their in-service training from outside, but could choose their providers to support their own needs.
One of the worst thing about academies is that the National Terms and Conditions will no longer apply, which is, of course, why the government want to go ahead. Schools will also be able to appoint unqualified teachers when finances are tight.
Academy chains are not allowed to make a profit, so what they do is set themselves up as charities and then establish a profit-making company to provide administrative services, such as payroll, HR, general management and advisory services. These companies are not subject to Freedom of Information requests and it has been estimated that approximately £3billion has been siphoned off to these companies from just three counties (Cumbria, Yorkshire and Lancashire). This is money which could have paid for teachers and classroom resources.