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Just add defaultValue parameter in CreateTable method for property:

public partial class TestSimpleEntity : DbMigration
    {
        public override void Up()
        {
            CreateTable(
                "dbo.SimpleEntities",
                c => new
                    {
                        id = c.Long(nullable: false, identity: true),
                        name = c.String(),
                        deleted = c.Boolean(nullable: false, defaultValue: true),
                    })
                .PrimaryKey(t => t.id);
            
        }
        
        public override void Down()
        {
            DropTable("dbo.SimpleEntities");
        }
}

After that, run update-database -verbose command, you will observe that EF will generate query which will contain Default value.

Below is the Table Definition from Server Explorer:

CREATE TABLE [dbo].[SimpleEntities] (
    [id]      BIGINT         IDENTITY (1, 1) NOT NULL,
    [name]    NVARCHAR (MAX) NULL,
    [deleted] BIT            DEFAULT ((1)) NOT NULL,
    CONSTRAINT [PK_dbo.SimpleEntities] PRIMARY KEY CLUSTERED ([id] ASC)
);

For the DateTime default value you can use defaultValueSql :

public partial class MyMigration : DbMigration
{
    public override void Up()
    {
        CreateTable("dbo.Users",
            c => new
                {
                    Created = c.DateTime(nullable: false, defaultValueSql: "GETDATE()"),
                })
            .PrimaryKey(t => t.ID);
 ...