From what I can tell, Epstein's trafficing operation did not houses the underage girls on his private Island for any long periods of time. Rather, they were brought in for guests during parties and were taken away sometime after the parties conclusions. Additionally, in the first case against Epstein, the matter was quickly plea barginned and the police chief involved in the case has said he was under pressure to not press the case, so it was likely the woefully inadequate plea deal didn't allow for the investigation to peruse the matter far enough to establish a probable cause that a search of the Island would yeild evidence to any of the crimes he was pleaing guilty to in that deal.
He was only arrested this time around when a new victim came forward. Again, it's not known if under-aged girls were kept on the island in any capacity beyond the parties, and I'm not even sure the girls involved were ever held against their will. The recent charges also do not name the Island as the scene of the crime, but rather residences in Manhatten's Upper East Side and Palm Beach, Florida only. Because no suspected crimes were alleged in the Virgin Islands' property, it's likely that there is little to any probable cause to execute a warrant there for evidence of the alleged crimes (and any such attempt would likely cause the evidence to be tossed out of court and compromise the investigation). Federal Law enforcement offices usually have a successful prosecution of all cases the bring against anyone, and rarely make arrests for federal crimes with out very convincing evidence. While it's still best to stick with innocence until proven guilty, I would advise betting against the Feds by the time they make an arrest against anyone. They normally have enough evidence of the charged crimes that the trial is mere formality (and remember, in the U.S. 90% of all crimes end in plea deals, regardless of Federal or State agency, so that's if you let it even get to that stage. Also, these stats are speaking to the quality of evidence collected with respect to the Reasonable Doubt standard needed to make a conviction, not any corruption of the prosecution and the judiciary). With that in mind, evidence on all 14 federal charges was likely good enough to get a conviction without the search of the Island.
One little discussed matter of Search Rights (or any rights in general in the United States) is they no long apply when you are deceased, to put the matter bluntly (less bluntly, is that the dead do not stand trial and the rights exist only if the evidence is someone is going to stand trial.). In this situation, a resident of the Island property could make the claim that it violates their privacy rights, but Epstein has no living family and was the sole resident of the property.
One final note as to why search now is that while Epstein's death was a suicide and Epstein more than likely killed himself, the conditions that allowed it to happen were highly irregular or out right grossly negligent for a Federal Prison. Coupled with the fact that this happened the day after several powerful people (The most powerful being Prince Andrew) were named as possible suspects for the first time publicly, there is a possibility that the laspses that allowed the suicide may have been deliberate. Again, the ridiculously good law enforcement at the Federal Level applies in this case as Epstein was the first suicide of an inmate in Federal Custody in 40 years. While I am want to say this was a malicious allowance of Epstein's death, I do understand it is probable that Epstein could have been the victim of some sort of foul play.
If the investigation has not ruled this out, then they are likely conducting the search of Epstein's Island as a search of a murder suspect's home, rather than a search of a convicted sex offender on a new round of charges. And in this aspect, any parties to Epstien's crimes can be prosecuted if evidence of their own participation is found on the property, as expressed by law enforcement agents close to the search (There was a news story where one agency put potential conspirators on notice that new evidence found there can be used against them if they are implicated in a crime. Even if they had nothing to do with Epstein's death.)