Special Education laws affect homeschoolers in several ways.
The first is the identification of the child as being elegible for services. Current law requires districts to offer testing to any child referred to them through the Child Find Program. Some homeschoolers want to ensure that they continue to have this right. Others want nothing to do with any government programs, especially ones that single their child out. In NH, parents have the right to home educate their special needs children with no more regulation than other children, and to refuse services. This is not true in all states. Once the child is identified, with the advent of national databases, that designation could follow him/her to any state where his/her parents relocate. The home education laws in that state might not permit the parent to do what s/he thinks is best for the child.
The second has to do with delivery of services. Under current federal and state law, in NH a parent's letter of intent to homeschool can be taken by the district, if it so chooses, as refusal of services. It is up to each district whether or not it will offer special education services to homeschooled children. This has a strange twist -- it is only during the years when compulsory attendance requires the parent to submit a letter of intent that the district can refuse services. Until the age of 6, districts must provide services to "homeschooled" children. (I have never investigated this issue as it applies to a child who turns 16.)
Many, many districts do provide special education services to homeschoolers. Some wish to work with the parent to provide the optimal learning environment for the child. Some see it as preventing problems down the road should the child re-enter the public school system. Some do so reluctantly, as part of a negotiated agreement when an unhappy parent withdraws the child from public school and his/her IEP, and threatens to sue the school for not following through on its legal obligations.