> Ideally, numeric pk columns in entity classes would be BigInteger

I meant, if they have scale 0

I can not reproduce your issue. I tried with the NetBeans 6.5 and the latest dev build. Both the regular entity class
and the PK class use BigInteger

Here is the database table I tried
CREATE TABLE "BUG153562_TABLE"
   (	"ID" NUMBER(22,0) NOT NULL ENABLE,
        "DERIVATION_ID" NUMBER(22,0) NOT NULL ENABLE,
	"COLUMN2" NUMBER(22,0),
	CONSTRAINT "TABLE1_PK" PRIMARY KEY ("ID", "DERIVATION_ID")
   );

Here's the generated code:
public class Bug153562Table implements Serializable {
    private static final long serialVersionUID = 1L;
    @EmbeddedId
    protected Bug153562TablePK bug153562TablePK;
    @Column(name = "COLUMN2")
    private BigInteger column2;
......
}

public class Bug153562TablePK implements Serializable {
    @Basic(optional = false)
    @Column(name = "ID", nullable = false)
    private BigInteger id;
    @Basic(optional = false)
    @Column(name = "DERIVATION_ID", nullable = false)
    private BigInteger derivationId;
........
}

Please provide me more info, such as, the SQL script, what kind of project you used, etc, if you still see the problem.

If you still see the problem, please reopen it with a reproducible case.

This problem is happening again in version 8.

Here the reproducible case using Oracle 11gXE and Netbeans 8.2 in MacOS Sierra:

CREATE TABLE "TEST" 
(
  "ID" NUMBER(38,0) NOT NULL ENABLE, 
  "CREATION" DATE NOT NULL ENABLE, 
  "CREATION_USR" VARCHAR2(255 CHAR) NOT NULL ENABLE, 
  CONSTRAINT "TEST_PK" PRIMARY KEY ("ID") ENABLE
);

And the generated class is:

@Entity
@Table(name = "TEST")
public class Test implements Serializable {

    private static final long serialVersionUID = 1L;

    @Id
    @Basic(optional = false)
    @NotNull
    @Column(name = "ID")
    private BigDecimal id;
    @Basic(optional = false)
    @NotNull
    @Column(name = "CREATION")
    @Temporal(TemporalType.TIMESTAMP)
    private Date creation;
    @Basic(optional = false)
    @NotNull
    @Size(min = 1, max = 255)
    @Column(name = "CREATION_USR")
    private String creationUsr;

    public Test() {
    }

    ...
}

and another case, when is and Embeddable PK is using BigInteger, if ID is the same in table TEST and TEST2 is causes problems:

CREATE TABLE "TEST2" 
(
  "ID1" NUMBER(38,0) NOT NULL ENABLE, 
  "ID2" NUMBER(38,0) NOT NULL ENABLE, 
  "CREATION" DATE NOT NULL ENABLE, 
  "CREATION_USR" VARCHAR2(255 CHAR) NOT NULL ENABLE, 
  CONSTRAINT "TEST2_PK" PRIMARY KEY ("ID1","ID2") ENABLE
);

and the class generated:

@Entity
@Table(name = "TEST2")
public class Test2 implements Serializable {

    private static final long serialVersionUID = 1L;
    @EmbeddedId
    protected Test2PK test2PK;
    @Basic(optional = false)
    @NotNull
    @Column(name = "CREATION")
    @Temporal(TemporalType.TIMESTAMP)
    private Date creation;
    @Basic(optional = false)
    @NotNull
    @Size(min = 1, max = 255)
    @Column(name = "CREATION_USR")
    private String creationUsr;

   ...
}

@Embeddable
public class Test2PK implements Serializable {

    @Basic(optional = false)
    @NotNull
    @Column(name = "ID1")
    private BigInteger id1;
    @Basic(optional = false)
    @NotNull
    @Column(name = "ID2")
    private BigInteger id2;

   ...
}