Currently Squeryl simply ignores fields of unsupported types in table classes. It should probably throw an exception of some sort for unannotated fields of unsupported types , and provide some sort of annotation to allow fields to exist in table classes that are ignored by Squeryl (like @transient to match the EJB3 persistence annotations).
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It looks like there's already an @transient annotation, so that part is already done!
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Test case (currently fails) :

package org.squeryl.tests

import org.specs.Specification

import org.squeryl.Schema
import org.squeryl.annotations.Transient

/**
 * Tests schema related functionality.
 */
class SchemaTests extends Specification
{
  "Schema" should {
    "reject empty record classes" in {
      class EmptyRecord {
      }
      object EmptyRecordSchema extends Schema {
        def tbl = table[EmptyRecord]
      }
    } must throwAn[IllegalArgumentException]

    "reject records with unsupported types" in {
      case class UnsupportedTypeRecord (unsupportedType :Thread) {
        def this() = this(null)
      }
      object UnsupportedTypeSchema extends Schema {
        def tbl = table[UnsupportedTypeRecord]
      }
      // should not be reached
    } must throwAn[IllegalArgumentException]

    "allow records with annotated types" in {
      case class AnnotatedUnsupportedTypeRecord (
        @Transient
        unsupportedType :Thread
      ) {
        def this() = this(null)
      }
      object AnnotatedUnsupportedTypeSchema extends Schema {
        def tbl = table[AnnotatedUnsupportedTypeRecord]
      }
      1 must be(1) // if we reach here, the test passed
    }
  }
}