I don't think you could delete 1000+ items in a single idiom in boto2 either. However, from boto3 perspective, you could try the following:
s3 = boto3.resource('s3')
bucket = s3.Bucket('bucket-name')
bucket.objects.filter(Prefix="path/to/dir").delete()
The above was tested and is working
>>> import boto3
>>> s3 = boto3.resource('s3')
>>> b = s3.Bucket('MY_BUCKET_NAME')
>>> b.objects.filter(Prefix="test/stuff")
s3.Bucket.objectsCollection(s3.Bucket(name='MY_BUCKET_NAME'), s3.ObjectSummary)
>>> list(b.objects.filter(Prefix="test/stuff"))
[s3.ObjectSummary(bucket_name='MY_BUCKET_NAME', key=u'test/stuff/new')]
>>> b.objects.filter(Prefix="test/stuff").delete()
[{u'Deleted': [{u'Key': 'test/stuff/new'}], 'ResponseMetadata': {'HTTPStatusCode': 200, 'RetryAttempts': 0, 'HostId': 'BASE64_ID_1', 'RequestId': 'REQ_ID', 'HTTPHeaders': {'x-amz-id-2': 'BASE64_ID_2', 'server': 'AmazonS3', 'transfer-encoding': 'chunked', 'connection': 'close', 'x-amz-request-id': 'REQ_ID', 'date': 'Fri, 12 May 2017 21:21:47 GMT', 'content-type': 'application/xml'}}}]
>>>